arXiv subjects

Christophe Phillips

Publications and source records attributed to Christophe Phillips.

8 recordsLinked to original sources

arXiv2026

Containerizing BIDSme : A Reproducible Tool for BIDS Conversion

The "Brain Imaging Data Structure" (BIDS) has become a widely adopted standard for organizing and sharing neuroimaging datasets of various modalities. However, converting raw brain imaging data into BIDS framework remains a complex and time-consuming task. BIDSme is a semi-automated tool developed to streamline this conversion process, but until recently, it lacked the portability and accessibility needed for widespread adoption. This paper presents the containerization of BIDSme using Docker and Docker Compose, improving usability, reproducibility, and integration into existing platforms like Neurodesk. It also details the design choices, iterative refinements, and validation process that led to a flexible, lightweight, and user-friendly containerized application.

cs.DB↗

arXiv2025

Elastic-Net Multiple Kernel Learning: Combining Multiple Data Sources for Prediction

Multiple Kernel Learning (MKL) models combine several kernels in supervised and unsupervised settings to integrate multiple data representations or sources, each represented by a different kernel. MKL seeks an optimal linear combination of base kernels that maximizes a generalized performance measure under a regularization constraint. Various norms have been used to regularize the kernel weights, including $l1$, $l2$ and $lp$, as well as the "elastic-net" penalty, which combines $l1$- and $l2$-norm to promote both sparsity and the selection of correlated kernels. This property makes elastic-net regularized MKL (ENMKL) especially valuable when model interpretability is critical and kernels capture correlated information, such as in neuroimaging. Previous ENMKL methods have followed a two-stage procedure: fix kernel weights, train a support vector machine (SVM) with the weighted kernel, and then update the weights via gradient descent, cutting-plane methods, or surrogate functions. Here, we introduce an alternative ENMKL formulation that yields a simple analytical update for the kernel weights. We derive explicit algorithms for both SVM and kernel ridge regression (KRR) under this framework, and implement them in the open-source Pattern Recognition for Neuroimaging Toolbox (PRoNTo). We evaluate these ENMKL algorithms against $l1$-norm MKL and against SVM (or KRR) trained on the unweighted sum of kernels across three neuroimaging applications. Our results show that ENMKL matches or outperforms $l1$-norm MKL in all tasks and only underperforms standard SVM in one scenario. Crucially, ENMKL produces sparser, more interpretable models by selectively weighting correlated kernels.

cs.LG↗

arXiv2024

A review of handcrafted and deep radiomics in neurological diseases: transitioning from oncology to clinical neuroimaging

Medical imaging technologies have undergone extensive development, enabling non-invasive visualization of clinical information. The traditional review of medical images by clinicians remains subjective, time-consuming, and prone to human error. With the recent availability of medical imaging data, quantification have become important goals in the field. Radiomics, a methodology aimed at extracting quantitative information from imaging data, has emerged as a promising approach to uncover hidden biological information and support decision-making in clinical practice. This paper presents a review of the radiomic pipeline from the clinical neuroimaging perspective, providing a detailed overview of each step with practical advice. It discusses the application of handcrafted and deep radiomics in neuroimaging, stratified by neurological diagnosis. Although radiomics shows great potential for increasing diagnostic precision and improving treatment quality in neurology, several limitations hinder its clinical implementation. Addressing these challenges requires collaborative efforts, advancements in image harmonization methods, and the establishment of reproducible and standardized pipelines with transparent reporting. By overcoming these obstacles, radiomics can significantly impact clinical neurology and enhance patient care.

eess.IV↗

arXiv2023

The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

q-bio.OT↗

arXiv2021

Shamo: A tool for electromagnetic modeling, simulation and sensitivity analysis of the head

Accurate electromagnetic modeling of the head of a subject is of main interest in the fields of source reconstruction and brain stimulation. Those processes rely heavily on the quality of the model and, even though the geometry of the tissues can be extracted from magnetic resonance images (MRI) or computed tomography (CT), their physical properties such as the electrical conductivity are hard to measure with non intrusive techniques. In this paper, we propose a tool to assess the uncertainty in the model parameters as well as compute a parametric electroencephalography (EEG) forward solution and current distribution for transcranial direct current stimulation (tDCS).

physics.med-ph↗

arXiv2014

Cerebral functional connectivity periodically (de)synchronizes with anatomical constraints

This paper studies the link between resting-state functional connectivity (FC), measured by the correlations of the fMRI BOLD time courses, and structural connectivity (SC), estimated through fiber tractography. Instead of a static analysis based on the correlation between SC and the FC averaged over the entire fMRI time series, we propose a dynamic analysis, based on the time evolution of the correlation between SC and a suitably windowed FC. Assessing the statistical significance of the time series against random phase permutations, our data show a pronounced peak of significance for time window widths around 20-30 TR (40-60 sec). Using the appropriate window width, we show that FC patterns oscillate between phases of high modularity, primarily shaped by anatomy, and phases of low modularity, primarily shaped by inter-network connectivity. Building upon recent results in dynamic FC, this emphasizes the potential role of SC as a transitory architecture between different highly connected resting state FC patterns. Finally, we show that networks implied in consciousness-related processes, such as the default mode network (DMN), contribute more to these brain-level fluctuations compared to other networks, such as the motor or somatosensory networks. This suggests that the fluctuations between FC and SC are capturing mind-wandering effects.

q-bio.NC↗

arXiv2013

Statistical tests for group comparison of manifold-valued data

Motivated by population studies of Diffusion Tensor Imaging, the paper investigates the use of mean-based and dispersion-based permutation tests to define and compute the significance of a statistical test for data taking values on nonlinear manifolds. The paper proposes statistical tests that are computationally tractable and geometrically sound for Diffusion Tensor Imaging.

math.ST↗

arXiv2012

An anisotropy preserving metric for DTI processing

Statistical analysis of Diffusion Tensor Imaging (DTI) data requires a computational framework that is both numerically tractable (to account for the high dimensional nature of the data) and geometric (to account for the nonlinear nature of diffusion tensors). Building upon earlier studies that have shown that a Riemannian framework is appropriate to address these challenges, the present paper proposes a novel metric and an accompanying computational framework for DTI data processing. The proposed metric retains the geometry and the computational tractability of earlier methods grounded in the affine invariant metric. In addition, and in contrast to earlier methods, it provides an interpolation method which preserves anisotropy, a central information carried by diffusion tensor data.

cs.CV↗