Many research applications of neuroimaging use magnetic resonance imaging (MRI). As such, recommendations for image analysis and standardized imaging pipelines exist. Clinical imaging, however, ...relies heavily on X-ray computed tomography (CT) scans for diagnosis and prognosis. Currently, there is only one image processing pipeline for head CT, which focuses mainly on head CT data with lesions. We present tools and a complete pipeline for processing CT data, focusing on open-source solutions, that focus on head CT but are applicable to most CT analyses. We describe going from raw DICOM data to a spatially normalized brain within CT presenting a full example with code. Overall, we recommend anonymizing data with Clinical Trials Processor, converting DICOM data to NIfTI using dcm2niix, using BET for brain extraction, and registration using a publicly-available CT template for analysis.
In analysis of binary outcomes, the receiver operator characteristic (ROC) curve is heavily used to show the performance of a model or algorithm. The ROC curve is informative about the performance ...over a series of thresholds and can be summarized by the area under the curve (AUC), a single number. When a
predictor
is categorical, the ROC curve has one less than number of categories as potential thresholds; when the predictor is binary, there is only one threshold. As the AUC may be used in decision-making processes on determining the best model, it important to discuss how it agrees with the intuition from the ROC curve. We discuss how the interpolation of the curve between thresholds with binary predictors can largely change the AUC. Overall, we show using a linear interpolation from the ROC curve with binary predictors corresponds to the estimated AUC, which is most commonly done in software, which we believe can lead to misleading results. We compare R, Python, Stata, and SAS software implementations. We recommend using reporting the interpolation used and discuss the merit of using the step function interpolator, also referred to as the “pessimistic” approach by Fawcett (
2006
).
Recent studies have illustrated that motion-related artifacts remain in resting-state fMRI (rs-fMRI) data even after common corrective processing procedures have been applied, but the extent to which ...head motion distorts the data may be modulated by the corrective approach taken. We compare two different methods for estimating nuisance signals from tissues not expected to exhibit BOLD fMRI signals of neuronal origin: 1) the more commonly used mean signal method and 2) the principal components analysis approach (aCompCor: Behzadi et al., 2007). Further, we investigate the added benefit of “scrubbing” (Power et al., 2012) following both methods. We demonstrate that the use of aCompCor removes motion artifacts more effectively than tissue-mean signal regression. In addition, inclusion of more components from anatomically defined regions of no interest better mitigates motion-related artifacts and improves the specificity of functional connectivity estimates. While scrubbing further attenuates motion-related artifacts when mean signals are used, scrubbing provides no additional benefit in terms of motion artifact reduction or connectivity specificity when using aCompCor.
•We compared PCA- and mean signal-based artifact reduction methods for rs-fMRI data.•PCA more effectively attenuated motion artifacts than mean signal.•PCA enhanced the specificity of functional connectivity compared to mean signal.•Scan scrubbing following PCA did not further reduce motion artifacts.
The ability of individuals to engage in physical activity is a critical component of overall health and quality of life. However, there is a natural decline in physical activity associated with the ...aging process. Establishing normative trends of physical activity in aging populations is essential to developing public health guidelines and informing clinical perspectives regarding individuals' levels of physical activity. Beyond overall quantity of physical activity, patterns regarding the timing of activity provide additional insights into latent health status. Wearable accelerometers, paired with statistical methods from functional data analysis, provide the means to estimate diurnal patterns in physical activity. To date, these methods have been only applied to study aging trends in populations based in the United States. Here, we apply curve registration and functional regression to 24 h activity profiles for 88,793 men (N = 39,255) and women (N = 49,538) ages 42-78 from the UK Biobank accelerometer study to understand how physical activity patterns vary across ages and by gender. Our analysis finds that daily patterns in both the volume of physical activity and probability of being active change with age, and that there are marked gender differences in these trends. This work represents the largest-ever population analyzed using tools of this kind, and suggest that aging trends in physical activity are reproducible in different populations across countries.
•The ciftiTools R package is a user-friendly interface for CIFTI and GIFTI files.•It supports reading, writing, visualization, math and manipulation.•The plots can be static or interactive, and can ...be embedded in R Markdown documents.•cifiTools bridges a gap between statistical tools in R and grayordinates data.
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There is significant interest in adopting surface- and grayordinate-based analysis of MR data for a number of reasons, including improved whole-cortex visualization, the ability to perform surface smoothing to avoid issues associated with volumetric smoothing, improved inter-subject alignment, and reduced dimensionality. The CIFTI grayordinate file format introduced by the Human Connectome Project further advances grayordinate-based analysis by combining gray matter data from the left and right cortical hemispheres with gray matter data from the subcortex and cerebellum into a single file. Analyses performed in grayordinate space are well-suited to leverage information shared across the brain and across subjects through both traditional analysis techniques and more advanced statistical methods, including Bayesian methods. The R statistical environment facilitates use of advanced statistical techniques, yet little support for grayordinates analysis has been previously available in R. Indeed, few comprehensive programmatic tools for working with CIFTI files have been available in any language. Here, we present the ciftiTools R package, which provides a unified environment for reading, writing, visualizing, and manipulating CIFTI files and related data formats. We illustrate ciftiTools’ convenient and user-friendly suite of tools for working with grayordinates and surface geometry data in R, and we describe how ciftiTools is being utilized to advance the statistical analysis of grayordinate-based functional MRI data.
•We introduce a moderated t-statistic for performing group-level fMRI analysis.•The approach helps alleviate problems related to small sample sizes.•The approach outperforms several standard ...approaches.•An R-package is introduced for application of the method to fMRI data.
In recent years, there has been significant criticism of functional magnetic resonance imaging (fMRI) studies with small sample sizes. The argument is that such studies have low statistical power, as well as reduced likelihood for statistically significant results to be true effects. The prevalence of these studies has led to a situation where a large number of published results are not replicable and likely false. Despite this growing body of evidence, small sample fMRI studies continue to be regularly performed; likely due to the high cost of scanning. In this report we investigate the use of a moderated t-statistic for performing group-level fMRI analysis to help alleviate problems related to small sample sizes. The proposed approach, implemented in the popular R-package LIMMA (linear models for microarray data), has found wide usage in the genomics literature for dealing with similar issues. Utilizing task-based fMRI data from the Human Connectome Project (HCP), we compare the performance of the moderated t-statistic with the standard t-statistic, as well as the pseudo t-statistic commonly used in non-parametric fMRI analysis. We find that the moderated t-test significantly outperforms both alternative approaches for studies with sample sizes less than 40 subjects. Further, we find that the results were consistent both when using voxel-based and cluster-based thresholding. We also introduce an R-package, LIMMI (linear models for medical images), that provides a quick and convenient way to apply the method to fMRI data.
Continuous Glucose Monitoring (CGM) data play an increasing role in clinical practice as they provide detailed quantification of blood glucose levels during the entire 24-hour period. The R package ...iglu implements a wide range of CGM-derived metrics for measuring glucose control and glucose variability. The package also allows one to visualize CGM data using time-series and lasagna plots. A distinct advantage of iglu is that it comes with a point-and-click graphical user interface (GUI) which makes the package widely accessible to users regardless of their programming experience. Thus, the open-source and easy to use iglu package will help advance CGM research and CGM data analyses. R package iglu is publicly available on CRAN and at https://github.com/irinagain/iglu.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary Background Intraventricular haemorrhage is a subtype of intracerebral haemorrhage, with 50% mortality and serious disability for survivors. We aimed to test whether attempting to remove ...intraventricular haemorrhage with alteplase versus saline irrigation improved functional outcome. Methods In this randomised, double-blinded, placebo-controlled, multiregional trial (CLEAR III), participants with a routinely placed extraventricular drain, in the intensive care unit with stable, non-traumatic intracerebral haemorrhage volume less than 30 mL, intraventricular haemorrhage obstructing the 3rd or 4th ventricles, and no underlying pathology were adaptively randomly assigned (1:1), via a web-based system to receive up to 12 doses, 8 h apart of 1 mg of alteplase or 0·9% saline via the extraventricular drain. The treating physician, clinical research staff, and participants were masked to treatment assignment. CT scans were obtained every 24 h throughout dosing. The primary efficacy outcome was good functional outcome, defined as a modified Rankin Scale score (mRS) of 3 or less at 180 days per central adjudication by blinded evaluators. This study is registered with ClinicalTrials.gov , NCT00784134. Findings Between Sept 18, 2009, and Jan 13, 2015, 500 patients were randomised: 249 to the alteplase group and 251 to the saline group. 180-day follow-up data were available for analysis from 246 of 249 participants in the alteplase group and 245 of 251 participants in the placebo group. The primary efficacy outcome was similar in each group (good outcome in alteplase group 48% vs saline 45%; risk ratio RR 1·06 95% CI 0·88–1·28; p=0·554). A difference of 3·5% (RR 1·08 95% CI 0·90–1·29, p=0·420) was found after adjustment for intraventricular haemorrhage size and thalamic intracerebral haemorrhage. At 180 days, the treatment group had lower case fatality (46 18% vs saline 73 29%, hazard ratio 0·60 95% CI 0·41–0·86, p=0·006), but a greater proportion with mRS 5 (42 17% vs 21 9%; RR 1·99 95% CI 1·22–3·26, p=0·007). Ventriculitis (17 7% alteplase vs 31 12% saline; RR 0·55 95% CI 0·31–0·97, p=0·048) and serious adverse events (114 46% alteplase vs 151 60% saline; RR 0·76 95% CI 0·64–0·90, p=0·002) were less frequent with alteplase treatment. Symptomatic bleeding (six 2% in the alteplase group vs five 2% in the saline group; RR 1·21 95% CI 0·37–3·91, p=0·771) was similar. Interpretation In patients with intraventricular haemorrhage and a routine extraventricular drain, irrigation with alteplase did not substantially improve functional outcomes at the mRS 3 cutoff compared with irrigation with saline. Protocol-based use of alteplase with extraventricular drain seems safe. Future investigation is needed to determine whether a greater frequency of complete intraventricular haemorrhage removal via alteplase produces gains in functional status. Funding National Institute of Neurological Disorders and Stroke.
Summary Background Craniotomy, according to the results from trials, does not improve functional outcome after intracerebral haemorrhage. Whether minimally invasive catheter evacuation followed by ...thrombolysis for clot removal is safe and can achieve a good functional outcome is not known. We investigated the safety and efficacy of alteplase, a recombinant tissue plasminogen activator, in combination with minimally invasive surgery (MIS) in patients with intracerebral haemorrhage. Methods MISTIE was an open-label, phase 2 trial that was done in 26 hospitals in the USA, Canada, the UK, and Germany. We used a computer-generated allocation sequence with a block size of four to centrally randomise patients aged 18–80 years with a non-traumatic (spontaneous) intracerebral haemorrhage of 20 mL or higher to standard medical care or image-guided MIS plus alteplase (0·3 mg or 1·0 mg every 8 h for up to nine doses) to remove clots using surgical aspiration followed by alteplase clot irrigation. Primary outcomes were all safety outcomes: 30 day mortality, 7 day procedure-related mortality, 72 h symptomatic bleeding, and 30 day brain infections. This trial is registered with ClinicalTrials.gov , number NCT00224770. Findings Between Feb 2, 2006, and April 8, 2013, 96 patients were randomly allocated and completed follow-up: 54 (56%) in the MIS plus alteplase group and 42 (44%) in the standard medical care group. The primary outcomes did not differ between the standard medical care and MIS plus alteplase groups: 30 day mortality (four 9·5%, 95% CI 2·7–22.6 vs eight 14·8%, 6·6–27·1, p=0·542), 7 day mortality (zero 0%, 0–8·4 vs one 1·9%, 0·1–9·9, p=0·562), symptomatic bleeding (one 2·4%, 0·1–12·6 vs five 9·3%, 3·1–20·3, p=0·226), and brain bacterial infections (one 2·4%, 0·1–12·6 vs zero 0%, 0–6·6, p=0·438). Asymptomatic haemorrhages were more common in the MIS plus alteplase group than in the standard medical care group (12 22·2%; 95% CI 12·0–35·6 vs three 7·1%; 1·5–19·5; p=0·051). Interpretation MIS plus alteplase seems to be safe in patients with intracerebral haemorrhage, but increased asymptomatic bleeding is a major cautionary finding. These results, if replicable, could lead to the addition of surgical management as a therapeutic strategy for intracerebral haemorrhage. Funding National Institute of Neurological Disorders and Stroke, Genentech, and Codman.
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