Image Quality Transfer of Diffusion MRI Guided By High-Resolution Structural MRI

Prior work on the Image Quality Transfer on Diffusion MRI (dMRI) has shown significant improvement over traditional interpolation methods. However, the difficulty in obtaining ultra-high resolution Diffusion MRI scans poses a problem in training neural networks to obtain high-resolution dMRI scans. Here we hypothesise that the inclusion of structural MRI images, which can be acquired at much higher resolutions, can be used as a guide to obtaining a more accurate high-resolution dMRI output. To test our hypothesis, we have constructed a novel framework that incorporates structural MRI scans together with dMRI to obtain high-resolution dMRI scans. We set up tests which evaluate the validity of our claim through various configurations and compare the performance of our approach against a unimodal approach. Our results show that the inclusion of structural MRI scans do lead to an improvement in high-resolution image prediction when T1w data is incorporated into the model input.

Tackling Structural Hallucination in Image Translation with Local Diffusion

Recent developments in diffusion models have advanced conditioned image generation, yet they struggle with reconstructing out-of-distribution (OOD) images, such as unseen tumors in medical images, causing ``image hallucination'' and risking misdiagnosis. We hypothesize such hallucinations result from local OOD regions in the conditional images. We verify that partitioning the OOD region and conducting separate image generations alleviates hallucinations in several applications. From this, we propose a training-free diffusion framework that reduces hallucination with multiple Local Diffusion processes. Our approach involves OOD estimation followed by two modules: a ``branching'' module generates locally both within and outside OOD regions, and a ``fusion'' module integrates these predictions into one. Our evaluation shows our method mitigates hallucination over baseline models quantitatively and qualitatively, reducing misdiagnosis by 40% and 25% in the real-world medical and natural image datasets, respectively. It also demonstrates compatibility with various pre-trained diffusion models.

A 3D Conditional Diffusion Model for Image Quality Transfer -- An Application to Low-Field MRI

Low-field (LF) MRI scanners (<1T) are still prevalent in settings with limited resources or unreliable power supply. However, they often yield images with lower spatial resolution and contrast than high-field (HF) scanners. This quality disparity can result in inaccurate clinician interpretations. Image Quality Transfer (IQT) has been developed to enhance the quality of images by learning a mapping function between low and high-quality images. Existing IQT models often fail to restore high-frequency features, leading to blurry output. In this paper, we propose a 3D conditional diffusion model to improve 3D volumetric data, specifically LF MR images. Additionally, we incorporate a cross-batch mechanism into the self-attention and padding of our network, ensuring broader contextual awareness even under small 3D patches. Experiments on the publicly available Human Connectome Project (HCP) dataset for IQT and brain parcellation demonstrate that our model outperforms existing methods both quantitatively and qualitatively. The code is publicly available at \url{https://github.com/edshkim98/DiffusionIQT}.

Domain-agnostic segmentation of thalamic nuclei from joint structural and diffusion MRI

The human thalamus is a highly connected subcortical grey-matter structure within the brain. It comprises dozens of nuclei with different function and connectivity, which are affected differently by disease. For this reason, there is growing interest in studying the thalamic nuclei in vivo with MRI. Tools are available to segment the thalamus from 1 mm T1 scans, but the contrast of the lateral and internal boundaries is too faint to produce reliable segmentations. Some tools have attempted to incorporate information from diffusion MRI in the segmentation to refine these boundaries, but do not generalise well across diffusion MRI acquisitions. Here we present the first CNN that can segment thalamic nuclei from T1 and diffusion data of any resolution without retraining or fine tuning. Our method builds on a public histological atlas of the thalamic nuclei and silver standard segmentations on high-quality diffusion data obtained with a recent Bayesian adaptive segmentation tool. We combine these with an approximate degradation model for fast domain randomisation during training. Our CNN produces a segmentation at 0.7 mm isotropic resolution, irrespective of the resolution of the input. Moreover, it uses a parsimonious model of the diffusion signal at each voxel (fractional anisotropy and principal eigenvector) that is compatible with virtually any set of directions and b-values, including huge amounts of legacy data. We show results of our proposed method on three heterogeneous datasets acquired on dozens of different scanners. An implementation of the method is publicly available at https://freesurfer.net/fswiki/ThalamicNucleiDTI.