MRI Super-Resolution using Multi-Channel Total Variation

This paper presents a generative model for super-resolution in routine clinical magnetic resonance images (MRI), of arbitrary orientation and contrast. The model recasts the recovery of high resolution images as an inverse problem, in which a forward model simulates the slice-select profile of the MR scanner. The paper introduces a prior based on multi-channel total variation for MRI super-resolution. Bias-variance trade-off is handled by estimating hyper-parameters from the low resolution input scans. The model was validated on a large database of brain images. The validation showed that the model can improve brain segmentation, that it can recover anatomical information between images of different MR contrasts, and that it generalises well to the large variability present in MR images of different subjects. The implementation is freely available at https://github.com/brudfors/spm_superre

Solid NURBS Conforming Scaffolding for Isogeometric Analysis

This work introduces a scaffolding framework to compactly parametrise solid structures with conforming NURBS elements for isogeometric analysis. A novel formulation introduces a topological, geometrical and parametric subdivision of the space in a minimal plurality of conforming vectorial elements. These determine a multi-compartmental scaffolding for arbitrary branching patterns. A solid smoothing paradigm is devised for the conforming scaffolding achieving higher than positional geometrical and parametric continuity. Results are shown for synthetic shapes of varying complexity, for modular CAD geometries, for branching structures from tessellated meshes and for organic biological structures from imaging data. Representative simulations demonstrate the validity of the introduced scaffolding framework with scalable performance and groundbreaking applications for isogeometric analysis

Elastic Registration of Geodesic Vascular Graphs

Vascular graphs can embed a number of high-level features, from morphological parameters, to functional biomarkers, and represent an invaluable tool for longitudinal and cross-sectional clinical inference. This, however, is only feasible when graphs are co-registered together, allowing coherent multiple comparisons. The robust registration of vascular topologies stands therefore as key enabling technology for group-wise analyses. In this work, we present an end-to-end vascular graph registration approach, that aligns networks with non-linear geometries and topological deformations, by introducing a novel overconnected geodesic vascular graph formulation, and without enforcing any anatomical prior constraint. The 3D elastic graph registration is then performed with state-of-the-art graph matching methods used in computer vision. Promising results of vascular matching are found using graphs from synthetic and real angiographies. Observations and future designs are discussed towards potential clinical applications

Machine prescription for chronic migraine

Responsive to treatment individually, chronic migraine remains strikingly resistant collectively, incurring the second-highest population burden of disability worldwide. A heterogeneity of responsiveness, requiring prolonged—currently heuristic—individual evaluation of available treatments, may reflect a diversity of causal mechanisms, or the failure to identify the most important, single causal factor. Distinguishing between these possibilities, now possible through the application of complex modelling to large-scale data, is critical to determining the optimal approach to identifying new interventions in migraine and making the best use of existing ones. Examining a richly phenotyped cohort of 1446 consecutive unselected patients with chronic migraine, here we use causal multitask Gaussian process models to estimate individual treatment effects across ten classes of preventatives. Such modelling enables us to quantify the accessibility of heterogeneous responsiveness to high-dimensional modelling, to infer the likely scale of the underlying causal diversity. We calculate the treatment effects in the overall population, and the conditional treatment effects among those modelled to respond and compare the true response rates between these two groups. Identifying a difference in response rates between the groups supports a diversity of causal mechanisms. Moreover, we propose a data-driven machine prescription policy, estimating the time-to-response when sequentially trialling preventatives by individualized treatment effects and compare it to expert guideline sequences. All model performances are quantified out-of-sample. We identify significantly higher true response rates among individuals modelled to respond, compared to the overall population (mean difference of 0.034; 95% confidence interval 0.003 to 0.065; p = 0.033), supporting significant heterogeneity of responsiveness and diverse causal mechanisms. The machine prescription policy yields an estimated 35% reduction in time-to-response (3.750 months; 95% confidence interval 3.507 to 3.993; p < 0.0001) compared with expert guidelines, with no substantive increase in expense per patient. We conclude that the highly distributed mode of causation in chronic migraine necessitates high-dimensional modelling for optimal management. Machine prescription should be considered an essential clinical decision-support tool in the future management of chronic migraine

Brain tumour segmentation with incomplete data

Brain tumour segmentation remains a challenging task, complicated by the marked heterogeneity of imaging appearances and their distribution across multiple modalities: FLAIR, T1-weighted, T2-weighted, and contrast-enhanced T1-weighted sequences (T1CE). This has compelled a research focus on uniformly multimodal models trained on complete acquisition sets rare in real-world clinical practice. Consider, for example, patients with renal failure who cannot receive contrast, artefact-spoiled sequences, or patients undergoing single-sequence intraoperative imaging. How well do segmentation models perform with such incomplete data, and what features of the lesion are identifiable under these circumstances? In a large-scale analysis involving 30 distinct segmentation models, we answer these questions with a state-of-the-art tumour segmentation modelling ensemble, nnU-Net-derived (Isensee et al, Nature Methods, 2020), deployed across all possible combinations of imaging modalities, trained, and tested with five-fold cross-validation on the 2021 BraTS-RSNA glioma population of 1251 patients. Segmentation performances for whole lesions range from Dice scores of 0.907 (single sequence) to 0.945 (full datasets) (Figure 1). When segmenting lesions by tissue type (enhancing tumour, non-enhancing tumour and oedema), Dice scores range from 0.701 (single sequence) to 0.891 (full datasets). Models missing postcontrast imaging still achieve a Dice coefficient for the whole tumour of 0.942 and identify the enhancing tumour component with Dice of up to 0.790 (Figure 2). Segmentation models can identify tumours with missing data, and can be used in clinical situations where partial data is frequent

Analyzing historical and future acute neurosurgical demand using an AI-enabled predictive dashboard

Characterizing acute service demand is critical for neurosurgery and other emergency-dominant specialties in order to dynamically distribute resources and ensure timely access to treatment. This is especially important in the post-Covid 19 pandemic period, when healthcare centers are grappling with a record backlog of pending surgical procedures and rising acute referral numbers. Healthcare dashboards are well-placed to analyze this data, making key information about service and clinical outcomes available to staff in an easy-to-understand format. However, they typically provide insights based on inference rather than prediction, limiting their operational utility. We retrospectively analyzed and prospectively forecasted acute neurosurgical referrals, based on 10,033 referrals made to a large volume tertiary neurosciences center in London, U.K., from the start of the Covid-19 pandemic lockdown period until October 2021 through the use of a novel AI-enabled predictive dashboard. As anticipated, weekly referral volumes significantly increased during this period, largely owing to an increase in spinal referrals (p < 0.05). Applying validated time-series forecasting methods, we found that referrals were projected to increase beyond this time-point, with Prophet demonstrating the best test and computational performance. Using a mixed-methods approach, we determined that a dashboard approach was usable, feasible, and acceptable among key stakeholders

Patch-CNN: Training data-efficient deep learning for high-fidelity diffusion tensor estimation from minimal diffusion protocols

We propose a new method, Patch-CNN, for diffusion tensor (DT) estimation from only six-direction diffusion weighted images (DWI). Deep learning-based methods have been recently proposed for dMRI parameter estimation, using either voxel-wise fully-connected neural networks (FCN) or image-wise convolutional neural networks (CNN). In the acute clinical context -- where pressure of time limits the number of imaged directions to a minimum -- existing approaches either require an infeasible number of training images volumes (image-wise CNNs), or do not estimate the fibre orientations (voxel-wise FCNs) required for tractogram estimation. To overcome these limitations, we propose Patch-CNN, a neural network with a minimal (non-voxel-wise) convolutional kernel (3$\times$3$\times$3). Compared with voxel-wise FCNs, this has the advantage of allowing the network to leverage local anatomical information. Compared with image-wise CNNs, the minimal kernel vastly reduces training data demand. Evaluated against both conventional model fitting and a voxel-wise FCN, Patch-CNN, trained with a single subject is shown to improve the estimation of both scalar dMRI parameters and fibre orientation from six-direction DWIs. The improved fibre orientation estimation is shown to produce improved tractogram.Comment: 12 pages, 6 figure