Brett Levac

Sriram Ravula, Brett Levac, Yamin Arefeen et al.

Magnetic resonance imaging (MRI) is a powerful medical imaging modality, but long acquisition times limit throughput, patient comfort, and clinical accessibility. Diffusion-based generative models serve as strong image priors for reducing scan-time with accelerated MRI reconstruction and offer robustness across variations in the acquisition model. However, most existing diffusion-based approaches do not exploit the unique ability in MRI to jointly design both the sampling pattern and the reconstruction method. While prior learning-based approaches have optimized sampling patterns for end-to-end unrolled networks, analogous methods for diffusion-based reconstruction have not been established due to the computational burden of posterior sampling. In this work, we propose a method to optimize k-space sampling patterns for accelerated multi-coil MRI reconstruction using diffusion models as priors. We introduce a training objective based on a single-step posterior mean estimate that avoids backpropagation through an expensive iterative reconstruction process. Then we present a greedy strategy for learning Cartesian sampling patterns that selects informative k-space locations using gradient information from a pre-trained diffusion model while enforcing spatial diversity among samples. Experimental results across multiple anatomies and acceleration factors demonstrate that diffusion models using the optimized sampling patterns achieve higher-quality reconstructions in comparison to using fixed and learned baseline patterns.

Asad Aali, Giannis Daras, Brett Levac et al.

We provide a framework for solving inverse problems with diffusion models learned from linearly corrupted data. Firstly, we extend the Ambient Diffusion framework to enable training directly from measurements corrupted in the Fourier domain. Subsequently, we train diffusion models for MRI with access only to Fourier subsampled multi-coil measurements at acceleration factors R= 2,4,6,8. Secondly, we propose Ambient Diffusion Posterior Sampling (A-DPS), a reconstruction algorithm that leverages generative models pre-trained on one type of corruption (e.g. image inpainting) to perform posterior sampling on measurements from a different forward process (e.g. image blurring). For MRI reconstruction in high acceleration regimes, we observe that A-DPS models trained on subsampled data are better suited to solving inverse problems than models trained on fully sampled data. We also test the efficacy of A-DPS on natural image datasets (CelebA, FFHQ, and AFHQ) and show that A-DPS can sometimes outperform models trained on clean data for several image restoration tasks in both speed and performance.

Yamin Arefeen, Brett Levac, Jonathan I. Tamir

We present the first acquisition-agnostic diffusion generative model for Magnetic Resonance Imaging (MRI) in the neonatal intensive care unit (NICU) to solve a range of inverse problems for shortening scan time and improving motion robustness. In-NICU MRI scanners leverage permanent magnets at lower field-strengths (i.e., below 1.5 Tesla) for non-invasive assessment of potential brain abnormalities during the critical phase of early live development, but suffer from long scan times and motion artifacts. In this setting, training data sizes are small and intrinsically suffer from low signal-to-noise ratio (SNR). This work trains a diffusion probabilistic generative model using such a real-world training dataset of clinical neonatal MRI by applying several novel signal processing and machine learning methods to handle the low SNR and low quantity of data. The model is then used as a statistical image prior to solve various inverse problems at inference time without requiring any retraining. Experiments demonstrate the generative model's utility for three real-world applications of neonatal MRI: accelerated reconstruction, motion correction, and super-resolution.

Yamin Arefeen, Brett Levac, Bhairav Patel et al.

Purpose: Magnetic Resonance Imaging (MRI) enables non-invasive assessment of brain abnormalities during early life development. Permanent magnet scanners operating in the neonatal intensive care unit (NICU) facilitate MRI of sick infants, but have long scan times due to lower signal-to-noise ratios (SNR) and limited receive coils. This work accelerates in-NICU MRI with diffusion probabilistic generative models by developing a training pipeline accounting for these challenges. Methods: We establish a novel training dataset of clinical, 1 Tesla neonatal MR images in collaboration with Aspect Imaging and Sha'are Zedek Medical Center. We propose a pipeline to handle the low quantity and SNR of our real-world dataset (1) modifying existing network architectures to support varying resolutions; (2) training a single model on all data with learned class embedding vectors; (3) applying self-supervised denoising before training; and (4) reconstructing by averaging posterior samples. Retrospective under-sampling experiments, accounting for signal decay, evaluated each item of our proposed methodology. A clinical reader study with practicing pediatric neuroradiologists evaluated our proposed images reconstructed from 1.5x under-sampled data. Results: Combining all data, denoising pre-training, and averaging posterior samples yields quantitative improvements in reconstruction. The generative model decouples the learned prior from the measurement model and functions at two acceleration rates without re-training. The reader study suggests that proposed images reconstructed from approximately 1.5x under-sampled data are adequate for clinical use. Conclusion: Diffusion probabilistic generative models applied with the proposed pipeline to handle challenging real-world datasets could reduce scan time of in-NICU neonatal MRI.

Brett Levac, Ajil Jalal, Kannan Ramchandran et al.

Blind inverse problems in imaging arise from uncertainties in the system used to collect (noisy) measurements of images. Recovering clean images from these measurements typically requires identifying the imaging system, either implicitly or explicitly. A common solution leverages generative models as priors for both the images and the imaging system parameters (e.g., a class of point spread functions). To learn these priors in a straightforward manner requires access to a dataset of clean images as well as samples of the imaging system. We propose an AmbientGAN-based generative technique to identify the distribution of parameters in unknown imaging systems, using only unpaired clean images and corrupted measurements. This learned distribution can then be used in model-based recovery algorithms to solve blind inverse problems such as blind deconvolution. We successfully demonstrate our technique for learning Gaussian blur and motion blur priors from noisy measurements and show their utility in solving blind deconvolution with diffusion posterior sampling.

Yamin Arefeen, Brett Levac, Zach Stoebner et al.

Implicit Neural Representations (INRs) are a learning-based approach to accelerate Magnetic Resonance Imaging (MRI) acquisitions, particularly in scan-specific settings when only data from the under-sampled scan itself are available. Previous work demonstrates that INRs improve rapid MRI through inherent regularization imposed by neural network architectures. Typically parameterized by fully-connected neural networks, INRs support continuous image representations by taking a physical coordinate location as input and outputting the intensity at that coordinate. Previous work has applied unlearned regularization priors during INR training and have been limited to 2D or low-resolution 3D acquisitions. Meanwhile, diffusion based generative models have received recent attention as they learn powerful image priors decoupled from the measurement model. This work proposes INFusion, a technique that regularizes the optimization of INRs from under-sampled MR measurements with pre-trained diffusion models for improved image reconstruction. In addition, we propose a hybrid 3D approach with our diffusion regularization that enables INR application on large-scale 3D MR datasets. 2D experiments demonstrate improved INR training with our proposed diffusion regularization, and 3D experiments demonstrate feasibility of INR training with diffusion regularization on 3D matrix sizes of 256 by 256 by 80.