arXiv subjects

Annalisa Pascarella

Publications and source records attributed to Annalisa Pascarella.

6 recordsLinked to original sources

arXiv2026

From Signals to Trajectories: A Primer on Low-Dimensional Dynamics in Human EEG and MEG

Neural activity unfolds not as a set of independent signals, but as a coordinated dynamical process that can be described as a point moving through a high-dimensional state space. This perspective has contributed substantially to recent developments in systems neuroscience, especially through studies of directly recorded neuronal population activity, but remains comparatively underused in non-invasive human recordings such as EEG and MEG. In this primer, we present a neural trajectory analysis based on Principal Component Analysis (PCA) as an accessible route into extending the concepts of neural trajectories in state space to human electrophysiology. We explain how EEG/MEG activity can be organized into neural state representations, projected onto axes organized by decreasing covariance, truncated into low-dimensional representations, and visualized as trajectories that capture how distributed activity evolves over time. We show how trajectory geometry can be used to compare conditions and relate neural dynamics to behavior or clinical outcomes. An example of EEG motor execution and imagery, accompanied by a tutorial notebook, illustrates the workflow from conventional EEG summaries to trajectory-based analysis. We also clarify the limits of PCA, including its linear, variance-driven nature, and discuss EEG/MEG-specific challenges such as spatial mixing, preprocessing sensitivity, validation, and overinterpretation. Finally, we situate PCA within a broader family of state-space methods. By making neural trajectories practical and interpretable, this primer offers a guide for bringing the conceptual framework of population-level dynamics into mainstream human cognitive neuroscience.

q-bio.NC↗

arXiv2026

A Roadmap for MEG Foundation Models

Foundation models are beginning to reshape brain-signal analysis by moving the field beyond task-specific decoding pipelines toward reusable models pretrained on broad neural datasets. Magnetoencephalography (MEG) is a compelling but still underdeveloped target for this shift: it captures human cortical dynamics at millisecond resolution while offering stronger spatial interpretability than EEG, making it especially valuable for source-resolved studies of perception, language, cognition, and clinical brain function. Yet MEG foundation models remain at an early stage, with only a small number of MEG-specific and MEG-inclusive multi-modal models, modest pretraining corpora, and emerging but still limited benchmarks. This perspective lays down the basic concepts needed to understand MEG foundation models and provides a didactic overview of the field's key design choices, including tokenization, sensor- versus source-space representations, sensor-geometry encoding, backbone architectures, self-supervised objectives, and pretraining data. We then offer a roadmap for future development, organized around native MEG pretraining, adaptation of EEG foundation models, transfer from generic time-series models, and multi-modal integration with EEG, fMRI, MRI, behaviour, and stimulus features. We highlight the need for coordinated infrastructure, including diverse and reusable MEG datasets, rigorous evaluation across subjects, sites, tasks, and clinical settings, and responsible data-sharing practices that address consent, privacy, access, and governance.

q-bio.NC↗

arXiv2025

Coord2Region: A Python Package for Mapping 3D Brain Coordinates to Atlas Labels, Literature, and AI Summaries

We present Coord2Region, an open-source Python package that streamlines coordinate-based neuroimaging workflows by automatically mapping 3D brain coordinates (e.g., MNI or Talairach) to anatomical regions across multiple atlases. The package links mapped coordinates to meta-analytic resources via the Neuroimaging Meta-Analysis Research Environment (NiMARE) , providing direct integration with Neurosynth and NeuroQuery. This directly connects coordinates and regions to the broader neuroimaging literature. In addition to atlas-based labeling and literature retrieval, Coord2Region offers an optional large language model (LLM) functionality that generates text summaries of linked studies and illustrative images of queried regions. These AI-assisted features are intended to support interpretation and exploration, while remaining clearly complementary to peer-reviewed literature and established neuroimaging tools. Coord2Region provides a unified pipeline with a robust command-line interface, flexible dataset management, and provider-agnostic LLM utilities, and it supports both single-coordinate and high-throughput batch queries with nearest-region fallback for volume and surface atlases. Furthermore, Coord2Region includes a web interface for interactive configuration (via JSON Schema forms) and cloud execution (via Hugging Face), enabling users to build YAML configurations and run analyses in-browser without local installation. Together, these capabilities lower friction, reduce manual errors, and improve reproducibility in coordinate-centric neuroimaging workflows, promoting more robust and transparent research practices.

q-bio.NC↗

arXiv2022

Parameter estimation tools for cardiovascular flow modeling of fetal circulation

Usually, clinicians assess the correct hemodynamic behavior and fetal well-being during the gestational age thanks to their professional expertise, with the support of some indices defined for Doppler fetal waveforms. Although this approach has demonstrated to be satisfactory in the most of the cases, it can be largely improved with the aid of more advanced techniques, i.e. numerical analysis and simulation. Another key aspect limiting the analysis is that clinicians rely on a limited number of Doppler waveforms observed during the clinical examination. Moreover, the use of simple velocimetric indicators for deriving possible malfunctions of the fetal cardiovascular system can be misleading, being the fetal assessment based on a mere statistical analysis (comparison with physiological ranges), without any deep physio-pathological interpretations of the observed hemodynamic changes. The use of a lumped mathematical model, properly describing the entire fetal cardiovascular system, would be absolutely helpful in this context: by targeting physiological model parameters on the clinical reliefs, we could gain deep insights of the full system. The calibration of model parameters may also help in formulating patient-specific early diagnosis of fetal pathologies. In the present work, we develop a robust parameter estimation algorithm based on two different optimization methods using synthetic data. In particular, we deal with the inverse problem of recognizing the most significant parameters of a lumped fetal circulation model by using time tracings of fetal blood flows and pressures obtained by the model. This represents a first methodological work for the assessment of the accuracy in the identification of model parameters of an algorithm based on closed-loop mathematical model of fetal circulation and opens the way to the application of the algorithm to clinical data.

physics.med-ph↗

arXiv2017

Brain activity mapping from MEG data via a hierarchical Bayesian algorithm with automatic depth weighting: sensitivity and specificity analysis

A recently proposed IAS MEG inverse solver algorithm, based on the coupling of a hierarchical Bayesian model with computationally efficient Krylov subspace linear solver, has been shown to perform well for both superficial and deep brain sources. However, a systematic study of its sensitivity and specificity as a function of the activity location is still missing. We propose novel statistical protocols to quantify the performance of MEG inverse solvers, focusing in particular on their sensitivity and specificity in identifying active brain regions. We use these protocols for a systematic study of the sensitivity and specificity of the IAS MEG inverse solver, comparing the performance with three standard inversion methods, wMNE, dSPM, and sLORETA. To avoid the bias of anecdotal tests towards a particular algorithm, the proposed protocols are Monte Carlo sampling based, generating an ensemble of activity patches in each brain region identified in a given atlas. The sensitivity is measured by how much, on average, the reconstructed activity is concentrated in the brain region of the simulated active patch. The specificity analysis is based on Bayes factors, interpreting the estimated current activity as data for testing the hypothesis that the active brain region is correctly identified, vs. the hypothesis of any erroneous attribution. The methodology allows the presence of a single or several simultaneous activity regions, without assuming the knowledge of the number of active regions. The testing protocols suggest that the IAS solver performs well in terms of sensitivity and specificity both with cortical and subcortical activity estimation.

q-bio.NC↗

arXiv2016

An inversion method based on random sampling for real-time MEG neuroimaging

The MagnetoEncephaloGraphy (MEG) has gained great interest in neurorehabilitation training due to its high temporal resolution. The challenge is to localize the active regions of the brain in a fast and accurate way. In this paper we use an inversion method based on random spatial sampling to solve the real-time MEG inverse problem. Several numerical tests on synthetic but realistic data show that the method takes just a few hundredths of a second on a laptop to produce an accurate map of the electric activity inside the brain. Moreover, it requires very little memory storage. For this reasons the random sampling method is particularly attractive in real-time MEG applications.

physics.med-ph↗