Uniform acquisition modelling across PET imaging systems: unified scatter modelling

RIN factor of all samples used for Illumina sequencing. (PDF 225 kb

Topological Surface States Protected From Backscattering by Chiral Spin Texture

Topological insulators are a new class of insulators in which a bulk gap for electronic excitations is generated by strong spin orbit coupling. These novel materials are distinguished from ordinary insulators by the presence of gapless metallic boundary states, akin to the chiral edge modes in quantum Hall systems, but with unconventional spin textures. Recently, experiments and theoretical efforts have provided strong evidence for both two- and three-dimensional topological insulators and their novel edge and surface states in semiconductor quantum well structures and several Bi-based compounds. A key characteristic of these spin-textured boundary states is their insensitivity to spin-independent scattering, which protects them from backscattering and localization. These chiral states are potentially useful for spin-based electronics, in which long spin coherence is critical, and also for quantum computing applications, where topological protection can enable fault-tolerant information processing. Here we use a scanning tunneling microscope (STM) to visualize the gapless surface states of the three-dimensional topological insulator BiSb and to examine their scattering behavior from disorder caused by random alloying in this compound. Combining STM and angle-resolved photoemission spectroscopy, we show that despite strong atomic scale disorder, backscattering between states of opposite momentum and opposite spin is absent. Our observation of spin-selective scattering demonstrates that the chiral nature of these states protects the spin of the carriers; they therefore have the potential to be used for coherent spin transport in spintronic devices.Comment: to be appear in Nature on August 9, 200

NiftyPET: Fast Quantitative Image Reconstruction for a New Brain PET Camera CareMiBrain

Fast and quantitative image reconstruction for a new dedicated brain PET camera, CareMiBrain, is presented using the open-source Python package NiftyPET. The camera consists of 48 monolithic LYSO crystals arranged in 3 rings of 16 detector modules each, with an effective 240 mm transaxial FOV and 152 mm axial FOV and resolution below 2 mm. The coordinates of any photon detection at each module are encoded using 96 96 virtual pixels, which are then written to list-mode (LM) data×for coincidence and single events. The image generation pipeline, from LM data processing to image reconstruction is performed on graphics processing units (GPU) using NiftyPET: First, the prompt LM data is processed producing 5184 sinograms in span-1 with 192 projection angles and 240 bins, while single events are used to estimate random event sinograms; the centre of mass of the radio-distribution in the projection space is used for motion detection with a temporal resolution of 1 second. The normalisation is performed using a scatter-free long acquisition of a dedicated ring phantom. Scatter correction is performed using a fully 3D voxel-driven scatter model (VSM); forward and back projections are calculated on the fly using the ray-driven Siddon algorithm. The above computations are performed using high-throughput GPU routines while enabling easy access for data quality checks at any point of the image generation pipeline. The quantitative performance was evaluated using the Derenzo and uniform cylindrical phantoms, demonstrating accurate corrections for photon attenuation, scatter and random events across a range of radioactivity doses

Uniform acquisition modelling across PET imaging systems: Unified scatter modelling

© 2016 IEEE. PET imaging is an important tool commonly used for studying disease by research consortia which implement multi-centre studies to improve the statistical power of findings. The UK government launched the Dementias Platform UK to facilitate one of the world's largest dementia population study involving national centres equipped with state-of-the-art PET/MR scanners from two major vendors. However, the difference in PET detector technology between the two scanners involved makes the standardisation of data acquisition and image reconstruction necessary. We propose a new approach to PET acquisition system modelling across different PET systems and technologies, focusing in particular on unified scatter estimation across TOF (time-of-flight) and non-TOF PET systems. The proposed scatter modelling is fully 3D and voxel based, as opposed to the popular line-of-response driven methods. This means that for each emitting voxel an independent 3D scatter estimate is found, inherently preserving the necessary information for TOF calculations as well as accounting for the large axial field of view. With adequate sampling of the input images, the non-TOF scatter estimate is identical to the summed TOF estimates across TOF bins, without an additional computational cost used for the TOF estimation. The model is implemented using the latest NVIDA GPU CUDA platform, allowing finer sampling of image space which is more essential for accurate TOF modelling. The high accuracy of the proposed scatter model is validated using Monte Carlo simulations. The model is deployed in our stand-alone image reconstruction pipeline for the Biograph mMR scanner, demonstrating accurate 3D scatter estimates resulting in uniform reconstruction for a high statistics phantom scan

Landmark-based evaluation of a block-matching registration framework on the RESECT pre- and intra-operative brain image data set

In this paper, we describe the application of an established block-matching based registration method to the CuRIOUS 2019 MICCAI registration challenge. Directional and symmetric approaches with different parameters are evaluated to select the most suitable setting of this fully automatic and general registration method. The results can be used as a baseline, for example when evaluating methods specialised in ultrasound (US) to MRI registration or registration of different interventional US (iUS) data. This work is a continuation of our contribution to the CuRIOUS 2018 challenge. We provide a more extensive analysis of main parameters as well as add pre- to post-resection iUS registration to the previous MRI-iUS registration. The proposed approach achieves an average target registration error of 2.68 mm and 1.92 mm for the MR-iUS and the iUS-iUS task respectively.</p

Parasympathetic nervous system dysfunction, as identified by pupil light reflex, and its possible connection to hearing impairment

Context Although the pupil light reflex has been widely used as a clinical diagnostic tool for autonomic nervous system dysfunction, there is no systematic review available to summarize the evidence that the pupil light reflex is a sensitive method to detect parasympathetic dysfunction. Meanwhile, the relationship between parasympathetic functioning and hearing impairment is relatively unknown. Objectives To 1) review the evidence for the pupil light reflex being a sensitive method to evaluate parasympathetic dysfunction, 2) review the evidence relating hearing impairment and parasympathetic activity and 3) seek evidence of possible connections between hearing impairment and the pupil light reflex. Methods Literature searches were performed in five electronic databases. All selected articles were categorized into three sections: pupil light reflex and parasympathetic dysfunction, hearing impairment and parasympathetic activity, pupil light reflex and hearing impairment. Results Thirty-eight articles were included in this review. Among them, 36 articles addressed the pupil light reflex and parasympathetic dysfunction. We summarized the information in these data according to different types of parasympathetic-related diseases. Most of the studies showed a difference on at least one pupil light reflex parameter between patients and healthy controls. Two articles discussed the relationship between hearing impairment and parasympathetic activity. Both studies reported a reduced parasympathetic activity in the hearing impaired groups. The searches identified no results for pupil light reflex and hearing impairment. Discussion and Conclusions As the first systematic review of the evidence, our findings suggest that the pupil light reflex is a sensitive tool to assess the presence of parasympathetic dysfunction. Maximum constriction velocity and relative constriction amplitude appear to be the most sensitive parameters. There are only two studies investigating the relationship between parasympathetic activity and hearing impairment, hence further research is needed. The pupil light reflex could be a candidate measurement tool to achieve this goal

Tau accumulation in autosomal dominant Alzheimer’s disease: a longitudinal [18F]flortaucipir study

Cortical tau accumulation is a key pathological event that partly defines Alzheimer’s disease (AD) onset and is associated with cognitive decline and future disease progression. However, an improved understanding of the timing and pattern of early tau deposition in AD and how this may be tracked in vivo is needed. Data from 59 participants involved in two longitudinal cohort studies of autosomal dominant AD (ADAD) were used to investigate whether tau PET can detect and track presymptomatic change; seven participants were symptomatic, and 52 were asymptomatic but at a 50% risk of carrying a pathogenic mutation. All had baseline flortaucipir (FTP) PET, MRI and clinical assessments; 26 individuals had more than one FTP PET scan. Standardised uptake value ratios (SUVRs) in prespecified regions of interest (ROIs) were obtained using inferior cerebellar grey matter as the reference region. We compared the changes in FTP SUVRs between presymptomatic carriers, symptomatic carriers and non-carriers, adjusting for age, sex and study site. We also investigated the relationship between regional FTP SUVRs and estimated years to/from symptom onset (EYO). Compared to both non-carriers and presymptomatic carriers, FTP SUVRs were significantly higher in symptomatic carriers in all ROIs tested (p 0.05), although increased FTP signal uptake was seen posteriorly in some individuals around the time of expected symptom onset. When we examined the relationship of FTP SUVR with respect to EYO, the earliest significant regional difference between mutation carriers and non-carriers was detected within the precuneus prior to estimated symptom onset in some cases. This study supports preliminary studies suggesting that presymptomatic tau tracer uptake is rare in ADAD. In cases where early uptake was seen, there was often a predilection for posterior regions (the precuneus and post-cingulate) as opposed to the medial temporal lobe, highlighting the importance of examining in vivo tau uptake beyond the confines of traditional Braak staging

An Automated and High Precision Quantitative Analysis of the ACR Phantom

A novel phantom-imaging platform for automated and high precision imaging of the American College of Radiology (ACR) PET phantom is proposed. The platform facilitates the generation of an accurate μ-map for PET/MR systems with a robust alignment based on two-stage image registration using specifically designed PET templates. The automated analysis of PET images uses a set of granular composite volume of interest (VOI) templates in a 0.5 mm resolution grid for sampling of the system response to the insert step functions. The impact of the activity outside the field of view (FOV) was evaluated using two acquisitions of 30 minutes each, with and without the activity outside the FOV. Iterative image reconstruction was employed with and without modelled shift-invariant point spread function (PSF) and varying ordered subsets expectation maximisation (OSEM) iterations. Uncertainty analysis of all image-derived statistics was performed using bootstrap resampling of the list-mode data. We found that the activity outside the FOV can adversely affect the imaging planes close to the edge of the axial FOV, reducing the contrast, background uniformity and overall quantitative accuracy. The PSF had a positive impact on contrast recovery (although it slows convergence). The proposed platform may be helpful in a more informative evaluation of PET systems and image reconstruction methods

Multi-tracer model for staging cortical amyloid deposition using PET imaging

OBJECTIVE: To develop and evaluate a model for staging cortical amyloid deposition using PET with high generalizability. METHODS: 3027 subjects (1763 Cognitively Unimpaired (CU), 658 Impaired, 467 Alzheimer's disease (AD) dementia, 111 non-AD dementia, and 28 with missing diagnosis) from six cohorts (EMIF-AD, ALFA, ABIDE, ADC, OASIS-3, ADNI) who underwent amyloid PET were retrospectively included; 1049 subjects had follow-up scans. Applying dataset-specific cut-offs to global Standard Uptake Value ratio (SUVr) values from 27 regions, single-tracer and pooled multi-tracer regional rankings were constructed from the frequency of abnormality across 400 CU subjects (100 per tracer). The pooled multi-tracer ranking was used to create a staging model consisting of four clusters of regions as it displayed a high and consistent correlation with each single-tracer ranking. Relationships between amyloid stage, clinical variables and longitudinal cognitive decline were investigated. RESULTS: SUVr abnormality was most frequently observed in cingulate, followed by orbitofrontal, precuneal, and insular cortices, then the associative, temporal and occipital regions. Abnormal amyloid levels based on binary global SUVr classification were observed in 1.0%, 5.5%, 17.9%, 90.0%, and 100.0% of stage 0-4 subjects, respectively. Baseline stage predicted decline in MMSE (ADNI: N=867, F=67.37, p3000 subjects across cohorts and radiotracers, and detects pre-global amyloid burden and distinct risk profiles of cognitive decline within globally amyloid-positive subjects