arXiv subjects

Maxime Chamberland

Publications and source records attributed to Maxime Chamberland.

11 recordsLinked to original sources

arXiv2026

SIINR: Structurally Informed Implicit Neural Representations for super-resolution with uncertainty quantification of clinical quality diffusion MRI datasets

Diffusion Magnetic Resonance Imaging (dMRI) is a powerful tool for probing brain microstructure, but clinical acquisitions are often limited by low out-of-plane resolution, resulting in degraded structural information and reduced utility for advanced analysis. We introduce SIINR (Structurally Informed Implicit Neural Representations), a general framework for super-resoltion of clinical dMRI datasets while quantifying uncertainty in the reconstructed outputs. SIINR utilizes a supervised 3D U-net as a prior and combines it with a self-supervised implicit neural representation (INR) that fuses the high-resolution prior and the original low-resolution data. The INR enables joint modeling across spatial and angular domains, enforces data consistency, and provides analytic approximate posterior distributions for downstream uncertainty quantification. We validate the framework on a diverse set of open-access dMRI datasets, demonstrating that SIINR outperforms standard interpolation methods in both quantitative error metrics and qualitative anatomical fidelity. Experiments on clinical cases, including subjects with multiple sclerosis and brain lesions, illustrate the framework its ability to propagate intensity changes and flag uncertain regions in challenging scenarios. SIINR is flexible, modular, and can be adapted to different upsampling ratios and downstream tasks, providing a principled approach for enhancing clinical dMRI and supporting robust interpretation of derived neuroimaging metrics.

cs.CV↗

arXiv2025

Connectivity-Preserving Cortical Surface Tetrahedralization

A prerequisite for many biomechanical simulation techniques is discretizing a bounded volume into a tetrahedral mesh. In certain contexts, such as cortical surface simulations, preserving input surface connectivity is critical. However, automated surface extraction often yields meshes containing self-intersections, small holes, and faulty geometry, which prevents existing constrained and unconstrained meshers from preserving this connectivity. We address this issue by developing a novel tetrahedralization method that maintains input surface connectivity in the presence of such defects. We also present a metric to quantify the preservation of surface connectivity and demonstrate that our method correctly maintains connectivity compared to existing solutions.

cs.CG↗

arXiv2025

Real-Time Rendering of Dynamic Line Sets using Voxel Ray Tracing

Real-time rendering of dynamic line sets is relevant in many visualization tasks, including unsteady flow visualization and interactive white matter reconstruction from Magnetic Resonance Imaging. High-quality global illumination and transparency are important for conveying the spatial structure of dense line sets, yet remain difficult to achieve at interactive rates. We propose an efficient voxel-based ray-tracing framework for rendering large dynamic line sets with ambient occlusion and ground-truth transparency. We introduce a voxelization algorithm that supports efficient on-the-fly construction of acceleration structures for both voxel cone tracing and ray tracing. To further reduce per-frame preprocessing cost, we propose a voxel-based culling method that restricts acceleration structure construction to camera-visible voxels. Together, these contributions enable real-time rendering of large-scale dynamic line sets with high quality and physically accurate transparency. We demonstrate that our method outperforms the state of the art in quality and performance when rendering (semi-)opaque dynamic line sets.

cs.GR↗

arXiv2025

Millennium Pathways for Tractography: 40 grand challenges to shape the future of tractography

In the spirit of the historic Millennium Prize Problems that heralded a new era for mathematics, the newly formed International Society for Tractography (IST) has launched the Millennium Pathways for Tractography, a community-driven roadmap designed to shape the future of the field. Conceived during the inaugural Tract-Anat Retreat, this initiative reflects a collective vision for advancing tractography over the coming decade and beyond. The roadmap consists of 40 grand challenges, developed by international experts and organized into seven categories spanning three overarching themes: neuroanatomy, tractography methods, and clinical applications. By defining shared short-, medium-, and long-term goals, these pathways provide a structured framework to confront fundamental limitations, promote rigorous validation, and accelerate the translation of tractography into a robust tool for neuroscience and medicine. Ultimately, the Millennium Pathways aim to guide and inspire future research and collaboration, ensuring the continued scientific and clinical relevance of tractography well into the future.

physics.med-ph↗

arXiv2025

Implicit neural representations for accurate estimation of the standard model of white matter

Diffusion magnetic resonance imaging (dMRI) enables non-invasive investigation of tissue microstructure. The Standard Model (SM) of white matter aims to disentangle dMRI signal contributions from intra- and extra-axonal water compartments. However, due to the model its high-dimensional nature, accurately estimating its parameters poses a complex problem and remains an active field of research, in which different (machine learning) strategies have been proposed. This work introduces an estimation framework based on implicit neural representations (INRs), which incorporate spatial regularization through the sinusoidal encoding of the input coordinates. The INR method is evaluated on both synthetic and in vivo datasets and compared to existing methods. Results demonstrate superior accuracy of the INR method in estimating SM parameters, particularly in low signal-to-noise conditions. Additionally, spatial upsampling of the INR can represent the underlying dataset anatomically plausibly in a continuous way. The INR is self-supervised, eliminating the need for labeled training data. It achieves fast inference, is robust to noise, supports joint estimation of SM kernel parameters and the fiber orientation distribution function with spherical harmonics orders up to at least 8, and accommodates gradient non-uniformity corrections. The combination of these properties positions INRs as a potentially important tool for analyzing and interpreting diffusion MRI data.

eess.IV↗

arXiv2024

MICCAI-CDMRI 2023 QuantConn Challenge Findings on Achieving Robust Quantitative Connectivity through Harmonized Preprocessing of Diffusion MRI

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

physics.med-ph↗

arXiv2024

Multi-dimensional Parameter Space Exploration for Streamline-specific Tractography

One of the unspoken challenges of tractography is choosing the right parameters for a given dataset or bundle. In order to tackle this challenge, we explore the multi-dimensional parameter space of tractography using streamline-specific parameters (SSP). We 1) validate a state-of-the-art probabilistic tracking method using per-streamline parameters on synthetic data, and 2) show how we can gain insights into the parameter space by focusing on streamline acceptance using real-world data. We demonstrate the potential added value of SSP to the current state of tractography by showing how SSP can be used to reveal patterns in the parameter space.

eess.IV↗

arXiv2023

Neural Spherical Harmonics for structurally coherent continuous representation of diffusion MRI signal

We present a novel way to model diffusion magnetic resonance imaging (dMRI) datasets, that benefits from the structural coherence of the human brain while only using data from a single subject. Current methods model the dMRI signal in individual voxels, disregarding the intervoxel coherence that is present. We use a neural network to parameterize a spherical harmonics series (NeSH) to represent the dMRI signal of a single subject from the Human Connectome Project dataset, continuous in both the angular and spatial domain. The reconstructed dMRI signal using this method shows a more structurally coherent representation of the data. Noise in gradient images is removed and the fiber orientation distribution functions show a smooth change in direction along a fiber tract. We showcase how the reconstruction can be used to calculate mean diffusivity, fractional anisotropy, and total apparent fiber density. These results can be achieved with a single model architecture, tuning only one hyperparameter. In this paper we also demonstrate how upsampling in both the angular and spatial domain yields reconstructions that are on par or better than existing methods.

eess.IV↗

arXiv2023

Voxlines: Streamline Transparency through Voxelization and View-Dependent Line Orders

As tractography datasets continue to grow in size, there is a need for improved visualization methods that can capture structural patterns occurring in large tractography datasets. Transparency is an increasingly important aspect of finding these patterns in large datasets but is inaccessible to tractography due to performance limitations. In this paper, we propose a rendering method that achieves performant rendering of transparent streamlines, allowing for exploration of deeper brain structures interactively. The method achieves this through a novel approximate order-independent transparency method that utilizes voxelization and caching view-dependent line orders per voxel. We compare our transparency method with existing tractography visualization software in terms of performance and the ability to capture deeper structures in the dataset.

cs.GR↗

arXiv2020

Tractometry-based Anomaly Detection for Single-subject White Matter Analysis

There is an urgent need for a paradigm shift from group-wise comparisons to individual diagnosis in diffusion MRI (dMRI) to enable the analysis of rare cases and clinically-heterogeneous groups. Deep autoencoders have shown great potential to detect anomalies in neuroimaging data. We present a framework that operates on the manifold of white matter (WM) pathways to learn normative microstructural features, and discriminate those at genetic risk from controls in a paediatric population.

q-bio.QM↗

arXiv2019

Reducing variability in along-tract analysis with diffusion profile realignment

Diffusion weighted MRI (dMRI) provides a non invasive virtual reconstruction of the brain's white matter structures through tractography. Analyzing dMRI measures along the trajectory of white matter bundles can provide a more specific investigation than considering a region of interest or tract-averaged measurements. However, performing group analyses with this along-tract strategy requires correspondence between points of tract pathways across subjects. This is usually achieved by creating a new common space where the representative streamlines from every subject are resampled to the same number of points. If the underlying anatomy of some subjects was altered due to, e.g. disease or developmental changes, such information might be lost by resampling to a fixed number of points. In this work, we propose to address the issue of possible misalignment, which might be present even after resampling, by realigning the representative streamline of each subject in this 1D space with a new method, coined diffusion profile realignment (DPR). Experiments on synthetic datasets show that DPR reduces the coefficient of variation for the mean diffusivity, fractional anisotropy and apparent fiber density when compared to the unaligned case. Using 100 in vivo datasets from the HCP, we simulated changes in mean diffusivity, fractional anisotropy and apparent fiber density. Pairwise Student's t-tests between these altered subjects and the original subjects indicate that regional changes are identified after realignment with the DPR algorithm, while preserving differences previously detected in the unaligned case. This new correction strategy contributes to revealing effects of interest which might be hidden by misalignment and has the potential to improve the specificity in longitudinal population studies beyond the traditional region of interest based analysis and along-tract analysis workflows.

q-bio.QM↗