Predicting Slice-to-Volume Transformation in Presence of Arbitrary Subject Motion

This paper aims to solve a fundamental problem in intensity-based 2D/3D registration, which concerns the limited capture range and need for very good initialization of state-of-the-art image registration methods. We propose a regression approach that learns to predict rotation and translations of arbitrary 2D image slices from 3D volumes, with respect to a learned canonical atlas co-ordinate system. To this end, we utilize Convolutional Neural Networks (CNNs) to learn the highly complex regression function that maps 2D image slices into their correct position and orientation in 3D space. Our approach is attractive in challenging imaging scenarios, where significant subject motion complicates reconstruction performance of 3D volumes from 2D slice data. We extensively evaluate the effectiveness of our approach quantitatively on simulated MRI brain data with extreme random motion. We further demonstrate qualitative results on fetal MRI where our method is integrated into a full reconstruction and motion compensation pipeline. With our CNN regression approach we obtain an average prediction error of 7mm on simulated data, and convincing reconstruction quality of images of very young fetuses where previous methods fail. We further discuss applications to Computed Tomography and X-ray projections. Our approach is a general solution to the 2D/3D initialization problem. It is computationally efficient, with prediction times per slice of a few milliseconds, making it suitable for real-time scenarios.Comment: 8 pages, 4 figures, 6 pages supplemental material, currently under review for MICCAI 201

Low temperature dynamics of kinks on Ising interfaces

The anisotropic motion of an interface driven by its intrinsic curvature or by an external field is investigated in the context of the kinetic Ising model in both two and three dimensions. We derive in two dimensions (2d) a continuum evolution equation for the density of kinks by a time-dependent and nonlocal mapping to the asymmetric exclusion process. Whereas kinks execute random walks biased by the external field and pile up vertically on the physical 2d lattice, then execute hard-core biased random walks on a transformed 1d lattice. Their density obeys a nonlinear diffusion equation which can be transformed into the standard expression for the interface velocity v = M[(gamma + gamma'')kappa + H]$, where M, gamma + gamma'', and kappa are the interface mobility, stiffness, and curvature, respectively. In 3d, we obtain the velocity of a curved interface near the orientation from an analysis of the self-similar evolution of 2d shrinking terraces. We show that this velocity is consistent with the one predicted from the 3d tensorial generalization of the law for anisotropic curvature-driven motion. In this generalization, both the interface stiffness tensor and the curvature tensor are singular at the orientation. However, their product, which determines the interface velocity, is smooth. In addition, we illustrate how this kink-based kinetic description provides a useful framework for studying more complex situations by modeling the effect of immobile dilute impurities.Comment: 11 pages, 10 figure

Role of computed tomography and magnetic resonance imaging in patients with cardiovascular disease

Background: Although there have been recent advances, cardiovascular disease remains the commonest cause of premature death in the United Kingdom. There is a need to develop safe non-invasive techniques to aid the diagnosis and treatment of patients with cardiovascular disease.Objectives: The aims of this thesis are: (i) to establish whether coronary artery calcification can be measured reproducibly by helical computed tomography; (ii) to establish the effect of lipid lowering therapy on the progression of coronary calcification; (iii) to determine whether multidetector computed tomography can predict graft patency in patients who have undergone coronary artery bypass grafting; and (iv), to investigate the role of magnetic resonance imaging to assess plaque characteristics following acute carotid plaque rupture.Methods: In 16 patients, coronary artery calcification was assessed twice within 4 weeks by helical computed tomography. As part of a randomised controlled trial, patients received atorvastatin 80 mg daily or matching placebo, and had coronary calcification assessed annually. Fifty patients with previous coronary artery bypass surgery who were listed for diagnostic coronary angiography underwent contrast enhanced computed tomography angiography using a 16-slice multidetector computed tomography scanner. Finally, 15 patients with recent symptoms and signs of an acute transient ischaemic attack, amaurosis fugax or stroke underwent magnetic resonance angiography of the carotid arteries using dedicated surface coils. Plaque volume, regional plaque densities and neovascularisation were determined before and after gadolinium enhancement.Results: Quantification of coronary artery calcification demonstrated good reproducibility in patients with scores > 100 AU. Despite reducing systemic inflammation and halving serum low-density lipoprotein cholesterol concentrations, atorvastatin therapy did not affect the rate of progression of coronary artery calcification. Computed tomography angiography was found to be highly specific for the detection of graft patency. Assessment of plaque characteristics by magnetic resonance scanning in patients with recent acute carotid plaque was feasible and reproducible.Conclusions: Coronary artery calcium scores can be determined in a reproducible manner. Although they correlate well with the presence of atherosclerosis and predict future coronary risk. there is little role for monitoring progression of coronary artery calcification in order to assess the response to lipid lowering therapy. Computed tomography can be used reliably to predict graft patency in patients who have undergone coronary artery bypass grafting, and is an acceptable non-invasive alternative to invasive coronary angiography. Magnetic resonance imaging techniques ' can be employed in a feasible, timely and reproducible manner to detect plaque characteristics associated with acute atherothrombotic disease

AFFIRM: Affinity Fusion-based Framework for Iteratively Random Motion correction of multi-slice fetal brain MRI

Multi-slice magnetic resonance images of the fetal brain are usually contaminated by severe and arbitrary fetal and maternal motion. Hence, stable and robust motion correction is necessary to reconstruct high-resolution 3D fetal brain volume for clinical diagnosis and quantitative analysis. However, the conventional registration-based correction has a limited capture range and is insufficient for detecting relatively large motions. Here, we present a novel Affinity Fusion-based Framework for Iteratively Random Motion (AFFIRM) correction of the multi-slice fetal brain MRI. It learns the sequential motion from multiple stacks of slices and integrates the features between 2D slices and reconstructed 3D volume using affinity fusion, which resembles the iterations between slice-to-volume registration and volumetric reconstruction in the regular pipeline. The method accurately estimates the motion regardless of brain orientations and outperforms other state-of-the-art learning-based methods on the simulated motion-corrupted data, with a 48.4% reduction of mean absolute error for rotation and 61.3% for displacement. We then incorporated AFFIRM into the multi-resolution slice-to-volume registration and tested it on the real-world fetal MRI scans at different gestation stages. The results indicated that adding AFFIRM to the conventional pipeline improved the success rate of fetal brain super-resolution reconstruction from 77.2% to 91.9%

Active swarms on a sphere

Here we show that coupling to curvature has profound effects on collective motion in active systems, leading to patterns not observed in flat space. Biological examples of such active motion in curved environments are numerous: curvature and tissue folding are crucial during gastrulation, epithelial and endothelial cells move on constantly growing, curved crypts and vili in the gut, and the mammalian corneal epithelium grows in a steady-state vortex pattern. On the physics side, droplets coated with actively driven microtubule bundles show active nematic patterns. We study a model of self-propelled particles with polar alignment on a sphere. Hallmarks of these motion patterns are a polar vortex and a circulating band arising due to the incompatibility between spherical topology and uniform motion - a consequence of the hairy ball theorem. We present analytical results showing that frustration due to curvature leads to stable elastic distortions storing energy in the band.Comment: 5 pages, 4 figures plus Supporting Informatio

Bulk Fields and Supersymmetry in a Slice of AdS

Five-dimensional models where the bulk is a slice of AdS have the virtue of solving the hierarchy problem. The electroweak scale is generated by a ``warp'' factor of the induced metric on the brane where the standard model fields live. However, it is not necessary to confine the standard model fields on the brane and we analyze the possibility of having the fields actually living in the slice of AdS. Specifically, we study the behaviour of fermions, gauge bosons and scalars in this geometry and their implications on electroweak physics. These scenarios can provide an explanation of the fermion mass hierarchy by warp factors. We also consider the case of supersymmetry in the bulk, and analyze the conditions on the mass spectrum. Finally, a model is proposed where the warp factor generates a small (TeV) supersymmetry-breaking scale, with the gauge interactions mediating the breaking to the scalar sector.Comment: 22 pages, 2 figures, LaTe