Cross-modality magnetic resonance (MR) image synthesis can be used to generate missing modalities from given ones. Existing (supervised learning) methods often require a large number of paired multi-modal data to train an effective synthesis model. However, it is often challenging to obtain sufficient paired data for supervised training. In reality, we often have a small number of paired data while a large number of unpaired data. To take advantage of both paired and unpaired data, in this paper, we propose a Multi-scale Transformer Network (MT-Net) with edge-aware pre-training for cross-modality MR image synthesis. Specifically, an Edge-preserving Masked AutoEncoder (Edge-MAE) is first pre-trained in a self-supervised manner to simultaneously perform 1) image imputation for randomly masked patches in each image and 2) whole edge map estimation, which effectively learns both contextual and structural information. Besides, a novel patch-wise loss is proposed to enhance the performance of Edge-MAE by treating different masked patches differently according to the difficulties of their respective imputations. Based on this proposed pre-training, in the subsequent fine-tuning stage, a Dual-scale Selective Fusion (DSF) module is designed (in our MT-Net) to synthesize missing-modality images by integrating multi-scale features extracted from the encoder of the pre-trained Edge-MAE. Further, this pre-trained encoder is also employed to extract high-level features from the synthesized image and corresponding ground-truth image, which are required to be similar (consistent) in the training. Experimental results show that our MT-Net achieves comparable performance to the competing methods even using $70\%$ of all available paired data. Our code will be publicly available at https://github.com/lyhkevin/MT-Net.
We present an algorithm for creating high resolution anatomically plausible images consistent with acquired clinical brain MRI scans with large inter-slice spacing. Although large data sets of clinical images contain a wealth of information, time constraints during acquisition result in sparse scans that fail to capture much of the anatomy. These characteristics often render computational analysis impractical as many image analysis algorithms tend to fail when applied to such images. Highly specialized algorithms that explicitly handle sparse slice spacing do not generalize well across problem domains. In contrast, we aim to enable application of existing algorithms that were originally developed for high resolution research scans to significantly undersampled scans. We introduce a generative model that captures fine-scale anatomical structure across subjects in clinical image collections and derive an algorithm for filling in the missing data in scans with large inter-slice spacing. Our experimental results demonstrate that the resulting method outperforms state-of-the-art upsampling super-resolution techniques, and promises to facilitate subsequent analysis not previously possible with scans of this quality. Our implementation is freely available at https://github.com/adalca/papago .
Very long baseline interferometry (VLBI) makes it possible to recover images of astronomical sources with extremely high angular resolution. Most recently, the Event Horizon Telescope (EHT) has extended VLBI to short millimeter wavelengths with a goal of achieving angular resolution sufficient for imaging the event horizons of nearby supermassive black holes. VLBI provides measurements related to the underlying source image through a sparse set spatial frequencies. An image can then be recovered from these measurements by making assumptions about the underlying image. One of the most important assumptions made by conventional imaging methods is that over the course of a night's observation the image is static. However, for quickly evolving sources, such as the galactic center's supermassive black hole (Sgr A*) targeted by the EHT, this assumption is violated and these conventional imaging approaches fail. In this work we propose a new way to model VLBI measurements that allows us to recover both the appearance and dynamics of an evolving source by reconstructing a video rather than a static image. By modeling VLBI measurements using a Gaussian Markov Model, we are able to propagate information across observations in time to reconstruct a video, while simultaneously learning about the dynamics of the source's emission region. We demonstrate our proposed Expectation-Maximization (EM) algorithm, StarWarps, on realistic synthetic observations of black holes, and show how it substantially improves results compared to conventional imaging algorithms. Additionally, we demonstrate StarWarps on real VLBI data of the M87 Jet from the VLBA.