Deep Learning using K-space Based Data Augmentation for Automated Cardiac MR Motion Artefact Detection

Quality assessment of medical images is essential for complete automation of image processing pipelines. For large population studies such as the UK Biobank, artefacts such as those caused by heart motion are problematic and manual identification is tedious and time-consuming. Therefore, there is an urgent need for automatic image quality assessment techniques. In this paper, we propose a method to automatically detect the presence of motion-related artefacts in cardiac magnetic resonance (CMR) images. As this is a highly imbalanced classification problem (due to the high number of good quality images compared to the low number of images with motion artefacts), we propose a novel k-space based training data augmentation approach in order to address this problem. Our method is based on 3D spatio-temporal Convolutional Neural Networks, and is able to detect 2D+time short axis images with motion artefacts in less than 1ms. We test our algorithm on a subset of the UK Biobank dataset consisting of 3465 CMR images and achieve not only high accuracy in detection of motion artefacts, but also high precision and recall. We compare our approach to a range of state-of-the-art quality assessment methods.Comment: Accepted for MICCAI2018 Conferenc

VLT/UVES Spectroscopy of Individual Stars in Three Globular Clusters in the Fornax Dwarf Spheroidal Galaxy

We present a high resolution (R ~ 43000) abundance analysis of a total of nine stars in three of the five globular clusters associated with the nearby Fornax dwarf spheroidal galaxy. These three clusters (1, 2 and 3) trace the oldest, most metal-poor stellar populations in Fornax. We determine abundances of O, Mg, Ca, Ti, Cr, Mn, Fe, Ni, Zn, Y, Ba, La, Nd and Eu in most of these stars, and for some stars also Mn and La. We demonstrate that classical indirect methods (isochrone fitting and integrated spectra) of metallicity determination lead to values of [Fe/H] which are 0.3 to 0.5 dex too high, and that this is primarily due to the underlying reference calibration typically used by these studies. We show that Cluster 1, with [Fe /H] = -2.5, now holds the record for the lowest metallicity globular cluster. We also measure an over-abundance of Eu in Cluster 3 stars that has only been previously detected in a subgroup of stars in M15. We find that the Fornax globular cluster properties are a global match to what is found in their Galactic counterparts; including deep mixing abundance patterns in two stars. We conclude that at the epoch of formation of globular clusters both the Milky Way and the Fornax dwarf spheroidal galaxy shared the same initial conditions, presumably pre-enriched by the same processes, with identical nucleosynthesis patterns.Comment: 16 pages, 12 figures. Accepted for publication in A&

MR-based respiratory and cardiac motion correction for PET imaging

Purpose: To develop a motion correction for Positron-Emission-Tomography (PET) using simultaneously acquired magnetic-resonance (MR) images within 90 s. Methods: A 90 s MR acquisition allows the generation of a cardiac and respiratory motion model of the body trunk. Thereafter, further diagnostic MR sequences can be recorded during the PET examination without any limitation. To provide full PET scan time coverage, a sensor fusion approach maps external motion signals (respiratory belt, ECG-derived respiration signal) to a complete surrogate signal on which the retrospective data binning is performed. A joint Compressed Sensing reconstruction and motion estimation of the subsampled data provides motion-resolved MR images (respiratory + cardiac). A 1-POINT DIXON method is applied to these MR images to derive a motion-resolved attenuation map. The motion model and the attenuation map are fed to the Customizable and Advanced Software for Tomographic Reconstruction (CASToR) PET reconstruction system in which the motion correction is incorporated. All reconstruction steps are performed online on the scanner via Gadgetron to provide a clinically feasible setup for improved general applicability. The method was evaluated on 36 patients with suspected liver or lung metastasis in terms of lesion quantification (SUVmax, SNR, contrast), delineation (FWHM, slope steepness) and diagnostic confidence level (3-point Likert-scale). Results: A motion correction could be conducted for all patients, however, only in 30 patients moving lesions could be observed. For the examined 134 malignant lesions, an average improvement in lesion quantification of 22%, delineation of 64% and diagnostic confidence level of 23% was achieved. Conclusion: The proposed method provides a clinically feasible setup for respiratory and cardiac motion correction of PET data by simultaneous short-term MRI. The acquisition sequence and all reconstruction steps are publicly available to fos

Molecular epidemiological investigation of a typhoid fever outbreak in South Africa, 2005: the relationship to a previous epidemic in 1993

In 2005, over 600 clinically diagnosed typhoid fever cases occurred in South Africa, where an outbreak had been previously described in 1993. Case-control and molecular investigations, including Salmonella enterica serovar Typhi (S. Typhi) isolates from that area from 1993, 2005 and later, were undertaken. Controls were significantly older than cases (P=0.003), possibly due to immunity from previous infection, and a significantly larger proportion had attended a gathering (P=0.035). Exposure to commercial food outlets and person-to-person transmission was not significant. Pulsed-field gel electrophoresis and multi-locus tandem repeat analysis revealed common clusters of S. Typhi strains identified in 1993 and 2005 as well as in 2007 and 2009. This outbreak probably occurred in a non-immune population due to faecally contaminated water. S. Typhi strains appeared to be related to strains from 1993; failure to address unsafe water may lead to further outbreaks in the area if the current population immunity wanes or is lost.This work was supported by a grant by the K. H. Keddy and others NHLS Research Trust