arXiv subjects

Antoine Théberge

Publications and source records attributed to Antoine Théberge.

5 recordsLinked to original sources

arXiv2026

A foundation for systematic analysis of transformers and RNNs for tractography

Machine learning (ML) has emerged as a promising approach for improving diffusion MRI (dMRI) tractography, a task that remains limited by the intrinsic tension between local diffusion information and global anatomical plausibility. In this work, we systematically evaluate recurrent neural networks (RNNs) and Transformer models for iterative tractography, with particular attention to training strategies, input representations (including convolutional neural network (CNN)-based embeddings and end-of-sequence (EOS) tokens), and hyperparameter selection. We introduce a generation-validation phase enabling supervision at the streamline level during training, allowing supervision despite the mismatch between local loss functions and global streamline quality. Using the ISMRM2015 tractography challenge dataset, our models achieve the highest reported performance to date. Through controlled experiments, we quantify the impact of missing bundles, noisy or imperfect training streamlines, and invalid fibers in the training set. Finally, we demonstrate the applicability of our best-performing models for in vivo data from the Tractoinferno database. Overall, our results highlight both the potential and the limits of sequence-based deep learning models such as Transformers and RNNs for tractography, and emphasize the need for improved phantoms and evaluation methods for in vivo validation. We provide takeaways and recommendations for future researchers training and validating sequence-based supervised methods for tractography.

cs.LG↗

arXiv2026

Exploring the robustness of TractOracle methods in RL-based tractography

Tractography algorithms leverage diffusion MRI to reconstruct the fibrous architecture of the brain's white matter. Among machine learning approaches, reinforcement learning (RL) has emerged as a promising framework for tractography, outperforming traditional methods in several key aspects. TractOracle-RL, a recent RL-based approach, reduces false positives by incorporating anatomical priors into the training process via a reward-based mechanism. In this paper, we investigate four extensions of the original TractOracle-RL framework by integrating recent advances in RL, and we evaluate their performance across five diverse diffusion MRI datasets. Results demonstrate that combining an oracle with the RL framework consistently leads to robust and reliable tractography, regardless of the specific method or dataset used. We also introduce a novel RL training scheme called Iterative Reward Training (IRT), inspired by the Reinforcement Learning from Human Feedback (RLHF) paradigm. Instead of relying on human input, IRT leverages bundle filtering methods to iteratively refine the oracle's guidance throughout training. Experimental results show that RL methods trained with oracle feedback significantly outperform widely used tractography techniques in terms of accuracy and anatomical validity.

cs.LG↗

arXiv2024

TractOracle: towards an anatomically-informed reward function for RL-based tractography

Reinforcement learning (RL)-based tractography is a competitive alternative to machine learning and classical tractography algorithms due to its high anatomical accuracy obtained without the need for any annotated data. However, the reward functions so far used to train RL agents do not encapsulate anatomical knowledge which causes agents to generate spurious false positives tracts. In this paper, we propose a new RL tractography system, TractOracle, which relies on a reward network trained for streamline classification. This network is used both as a reward function during training as well as a mean for stopping the tracking process early and thus reduce the number of false positive streamlines. This makes our system a unique method that evaluates and reconstructs WM streamlines at the same time. We report an improvement of true positive ratios by almost 20\% and a reduction of 3x of false positive ratios on one dataset and an increase between 2x and 7x in the number true positive streamlines on another dataset.

cs.LG↗

arXiv2023

What Matters in Reinforcement Learning for Tractography

Recently, deep reinforcement learning (RL) has been proposed to learn the tractography procedure and train agents to reconstruct the structure of the white matter without manually curated reference streamlines. While the performances reported were competitive, the proposed framework is complex, and little is still known about the role and impact of its multiple parts. In this work, we thoroughly explore the different components of the proposed framework, such as the choice of the RL algorithm, seeding strategy, the input signal and reward function, and shed light on their impact. Approximately 7,400 models were trained for this work, totalling nearly 41,000 hours of GPU time. Our goal is to guide researchers eager to explore the possibilities of deep RL for tractography by exposing what works and what does not work with the category of approach. As such, we ultimately propose a series of recommendations concerning the choice of RL algorithm, the input to the agents, the reward function and more to help future work using reinforcement learning for tractography. We also release the open source codebase, trained models, and datasets for users and researchers wanting to explore reinforcement learning for tractography.

cs.LG↗

arXiv2021

Manifold-aware Synthesis of High-resolution Diffusion from Structural Imaging

The physical and clinical constraints surrounding diffusion-weighted imaging (DWI) often limit the spatial resolution of the produced images to voxels up to 8 times larger than those of T1w images. Thus, the detailed information contained in T1w imagescould help in the synthesis of diffusion images in higher resolution. However, the non-Euclidean nature of diffusion imaging hinders current deep generative models from synthesizing physically plausible images. In this work, we propose the first Riemannian network architecture for the direct generation of diffusion tensors (DT) and diffusion orientation distribution functions (dODFs) from high-resolution T1w images. Our integration of the Log-Euclidean Metric into a learning objective guarantees, unlike standard Euclidean networks, the mathematically-valid synthesis of diffusion. Furthermore, our approach improves the fractional anisotropy mean squared error (FA MSE) between the synthesized diffusion and the ground-truth by more than 23% and the cosine similarity between principal directions by almost 5% when compared to our baselines. We validate our generated diffusion by comparing the resulting tractograms to our expected real data. We observe similar fiber bundles with streamlines having less than 3% difference in length, less than 1% difference in volume, and a visually close shape. While our method is able to generate high-resolution diffusion images from structural inputs in less than 15 seconds, we acknowledge and discuss the limits of diffusion inference solely relying on T1w images. Our results nonetheless suggest a relationship between the high-level geometry of the brain and the overall white matter architecture.

cs.CV↗