Anatomical Token Uncertainty for Transformer-Guided Active MRI Acquisition
This work addresses MRI acquisition speed for clinical applications, offering an incremental improvement over existing compressed sensing methods.
The paper tackles the slow acquisition problem in MRI by proposing an active sampling framework that uses token entropy from a pretrained medical image tokenizer and latent transformer to guide sampling, achieving state-of-the-art performance on fastMRI datasets at 8x and 16x acceleration with improvements in perceptual metrics and feature-based distances.
Full data acquisition in MRI is inherently slow, which limits clinical throughput and increases patient discomfort. Compressed Sensing MRI (CS-MRI) seeks to accelerate acquisition by reconstructing images from under-sampled k-space data, requiring both an optimal sampling trajectory and a high-fidelity reconstruction model. In this work, we propose a novel active sampling framework that leverages the inherent discrete structure of a pretrained medical image tokenizer and a latent transformer. By representing anatomy through a dictionary of quantized visual tokens, the model provides a well-defined probability distribution over the latent space. We utilize this distribution to derive a principled uncertainty measure via token entropy, which guides the active sampling process. We introduce two strategies to exploit this latent uncertainty: (1) Latent Entropy Selection (LES), projecting patch-wise token entropy into the $k$-space domain to identify informative sampling lines, and (2) Gradient-based Entropy Optimization (GEO), which identifies regions of maximum uncertainty reduction via the $k$-space gradient of a total latent entropy loss. We evaluate our framework on the fastMRI singlecoil Knee and Brain datasets at $\times 8$ and $\times 16$ acceleration. Our results demonstrate that our active policies outperform state-of-the-art baselines in perceptual metrics, and feature-based distances. Our code is available at https://github.com/levayz/TRUST-MRI.