A Theoretical Investigation of the Relationship between Structural Equation Modeling and Partial Correlation in Functional MRI Effective Connectivity

An important field of blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) is the investigation of effective connectivity, that is, the actions that a given set of regions exert on one another. We recently proposed a data-driven method based on the partial correlation matrix that could provide some insight regarding the pattern of functional interaction between brain regions as represented by structural equation modeling (SEM). So far, the efficiency of this approach was mostly based on empirical evidence. In this paper, we provide theoretical fundaments explaining why and in what measure structural equation modeling and partial correlations are related. This gives better insight regarding what parts of SEM can be retrieved by partial correlation analysis and what remains inaccessible. We illustrate the different results with real data

Phase Aberration Correction without Reference Data: An Adaptive Mixed Loss Deep Learning Approach

Phase aberration is one of the primary sources of image quality degradation in ultrasound, which is induced by spatial variations in sound speed across the heterogeneous medium. This effect disrupts transmitted waves and prevents coherent summation of echo signals, resulting in suboptimal image quality. In real experiments, obtaining non-aberrated ground truths can be extremely challenging, if not infeasible. It hinders the performance of deep learning-based phase aberration correction techniques due to sole reliance on simulated data and the presence of domain shift between simulated and experimental data. Here, for the first time, we propose a deep learning-based method that does not require reference data to compensate for the phase aberration effect. We train a network wherein both input and target output are randomly aberrated radio frequency (RF) data. Moreover, we demonstrate that a conventional loss function such as mean square error is inadequate for training the network to achieve optimal performance. Instead, we propose an adaptive mixed loss function that employs both B-mode and RF data, resulting in more efficient convergence and enhanced performance. Source code is available at \url{http://code.sonography.ai}

Estimation of the Hemodynamic Response Function in event-related functional MRI: directed acyclic graphs for a general Bayesian inference framework.

International audienceA convenient way to analyze BOLD fMRI data consists of modeling the whole brain as a stationary, linear system characterized by its transfer function: the Hemodynamic Response Function (HRF). HRF estimation, though of the greatest interest, is still under investigation, for the problem is ill-conditioned. In this paper, we recall the most general Bayesian model for HRF estimation and show how it can beneficially be translated in terms of graphical models, leading to (i) a clear and efficient representation of all structural and functional relationships entailed by the model, and (ii) a straightforward numerical scheme to approximate the joint posterior distribution, allowing for estimation of the HRF, as well as all other model parameters. We finally apply this novel technique on both simulations and real data

Estimation of the hemodynamic response in event-related functional MRI: Bayesian networks as a framework for efficient Bayesian modeling and inference.

International audienceA convenient way to analyze blood-oxygen-level-dependent functional magnetic resonance imaging data consists of modeling the whole brain as a stationary, linear system characterized by its transfer function: the hemodynamic response function (HRF). HRF estimation, though of the greatest interest, is still under investigation, for the problem is ill-conditioned. In this paper, we recall the most general Bayesian model for HRF estimation and show how it can beneficially be translated in terms of Bayesian graphical models, leading to 1) a clear and efficient representation of all structural and functional relationships entailed by the model, and 2) a straightforward numerical scheme to approximate the joint posterior distribution, allowing for estimation of the HRF, as well as all other model parameters. We finally apply this novel technique on both simulations and real data

Phase Aberration Correction: A Deep Learning-Based Aberration to Aberration Approach

One of the primary sources of suboptimal image quality in ultrasound imaging is phase aberration. It is caused by spatial changes in sound speed over a heterogeneous medium, which disturbs the transmitted waves and prevents coherent summation of echo signals. Obtaining non-aberrated ground truths in real-world scenarios can be extremely challenging, if not impossible. This challenge hinders training of deep learning-based techniques' performance due to the presence of domain shift between simulated and experimental data. Here, for the first time, we propose a deep learning-based method that does not require ground truth to correct the phase aberration problem, and as such, can be directly trained on real data. We train a network wherein both the input and target output are randomly aberrated radio frequency (RF) data. Moreover, we demonstrate that a conventional loss function such as mean square error is inadequate for training such a network to achieve optimal performance. Instead, we propose an adaptive mixed loss function that employs both B-mode and RF data, resulting in more efficient convergence and enhanced performance. Finally, we publicly release our dataset, including 161,701 single plane-wave images (RF data). This dataset serves to mitigate the data scarcity problem in the development of deep learning-based techniques for phase aberration correction.Comment: arXiv admin note: text overlap with arXiv:2303.0574

Complex dynamics for the study of neural activity in the human brain

Congrès sous l’égide de la Société Française de Génie Biologique et Médical (SFGBM).National audienceNeural mass modeling is a part of computational neuroscience that was developed to study the general behavior of interacting neuronal populations. This type of mesoscopic model is able to generate output signals that are comparable with experimental data such as electroencephalograms. Classically, neural mass models consider two interconnected populations. One interaction have been modeled in two differents ways. In this work we propose and analyze a neural mass model embedding both approaches and compare the generated time series to real data

Robust Bayesian estimation of the hemodynamic response function in event-related BOLD fMRI using basic physiological information.

International audienceIn BOLD fMRI data analysis, robust and accurate estimation of the Hemodynamic Response Function (HRF) is still under investigation. Parametric methods assume the shape of the HRF to be known and constant throughout the brain, whereas non-parametric methods mostly rely on artificially increasing the signal-to-noise ratio. We extend and develop a previously proposed method that makes use of basic yet relevant temporal information about the underlying physiological process of the brain BOLD response in order to infer the HRF in a Bayesian framework. A general hypothesis test is also proposed, allowing to take advantage of the knowledge gained regarding the HRF to perform activation detection. The performances of the method are then evaluated by simulation. Great improvement is shown compared to the Maximum-Likelihood estimate in terms of estimation error, variance, and bias. Robustness of the estimators with regard to the actual noise structure or level, as well as the stimulus sequence, is also proven. Lastly, fMRI data with an event-related paradigm are analyzed. As suspected, the regions selected from highly discriminating activation maps resulting from the method exhibit a certain inter-regional homogeneity in term of HRF shape, as well as noticeable inter-regional differences