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Neuroimaging has been facing a data deluge characterized by the exponential growth of both raw and processed data. As a result, mining the massive quantities of digital data collected in these studies offers unprecedented opportunities and has become paramount for today's research. As the neuroimaging community enters the world of “Big Data”, there has been a concerted push for enhanced sharing initiatives, whether within a multisite study, across studies, or federated and shared publicly. This article will focus on the database and processing ecosystem developed at the Montreal Neurological Institute (MNI) to support multicenter data acquisition both nationally and internationally, create database repositories, facilitate data-sharing initiatives, and leverage existing software toolkits for large-scale data processing. [ABSTRACT FROM AUTHOR]

This paper presents the Virtual Imaging Platform (VIP), a platform accessible at xlink:type="simple" xlink:href="http://vip.creatis.insa-lyon.fr" xmlns:xlink="http://www.w3.org/1999/xlink"http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011. [ABSTRACT FROM PUBLISHER]

Abstract: Pilot-job systems emerged as a computation paradigm to cope with the heterogeneity of large-scale production grids, greatly reducing fault ratios and middleware overheads. They are now widely adopted to sustain the computation of scientific applications on such platforms. However, a model of pilot-job systems is still lacking, making it difficult to build realistic experimental setups for their study (e.g. simulators or controlled platforms). The variability of production conditions, background loads and resource characteristics further complicate this issue. This paper presents a model of pilot-job resource provisioning. Based on a probabilistic modeling of pilot submission and registration, the number of pilots registered to the application host and the makespan of a divisible-load application are derived. The model takes into account job failures and it does not make any assumption on the characteristics of the computing resources, on the scheduling algorithm or on the background load. Only a minimally invasive monitoring of the grid is required. The model is evaluated in production conditions, using logs acquired on a pilot-job server deployed in the biomed virtual organization of the European Grid Infrastructure. Experimental results show that the model is able to accurately describe the number of registered pilots along time periods ranging from a few hours to a few days and in different pilot submission conditions. [Copyright &y& Elsevier]

Abstract: In this paper, we study grid jobs latency. Together with outliers, latency highly impacts applications performance on production grids, due to its order of magnitude and important variations. It is particularly prejudicial for determining the expected duration of applications handling a high number of jobs and it makes outliers detection difficult. In a previous work, a probabilistic model of the latency has been used to estimate an optimal timeout value considering a given distribution of jobs latencies. This timeout value is then used in a job resubmission strategy. The purpose of this paper is to evaluate to what extent updating this model with relevant contextual parameters can help to refine the latency estimation. In the first part of the paper, we study the validity of parameters along several weeks. Experiments on the EGEE production grid show that performance can be improved by updating model parameters. In the second part, we study the influence of the resource broker or the computing site and the day of the week. We experimentally show that some of them have a statistically significant influence on the job latency. We exploit this contextual information in the perspective of improving job submission strategies. [Copyright &y& Elsevier]

The article discusses various requirements for the application of workflow management systems. These requirements, accordingly, are needed for the creation of a system that would allow both a simple description of the dataflow of the application and an efficient execution on a grid platform. They include expressive and user-friendly workflow description with an efficient execution of data-sensitive scientific applications. Out of these requirements is the launching of MOTEUR, one known novel workflow engine that combines expressive workflow description with efficient grid execution. MOTEUR includes new algorithms that handle data synchronization barriers and data composition strategies in a fully parallel environment.

Semantic memory representations are generally well maintained in aging, whereas semantic control is thought to be more affected. To explain this phenomenon, this study tested the predictions of the Compensation-Related Utilization of Neural Circuits Hypothesis (CRUNCH), focusing on task demands in aging as a possible framework. The CRUNCH effect would manifest itself in semantic tasks through a compensatory increase in neural activation in semantic control network regions but only up to a certain threshold of task demands. This study compares 39 younger (20–35 years old) with 39 older participants (60–75 years old) in a triad-based semantic judgment task performed in an fMRI scanner while manipulating task demand levels (low versus high) through semantic distance. In line with the CRUNCH predictions, differences in neurofunctional activation and behavioral performance (accuracy and response times) were expected in younger versus older participants in the low- versus high-demand conditions, which should be manifested in semantic control Regions of Interest (ROIs). Our older participants had intact behavioral performance, as proposed in the literature for semantic memory tasks (maintained accuracy and slower response times (RTs)). Age-invariant behavioral performance in the older group compared to the younger one is necessary to test the CRUNCH predictions. The older adults were also characterized by high cognitive reserve, as our neuropsychological tests showed. Our behavioral results confirmed that our task successfully manipulated task demands: error rates, RTs and perceived difficulty increased with increasing task demands in both age groups. We did not find an interaction between age group and task demand, or a statistically significant difference in activation between the low- and high-demand conditions for either RTs or accuracy. As for brain activation, we did not find the expected age group by task demand interaction, or a significant main effect of task demand. Overall, our results are compatible with some neural activation in the semantic network and the semantic control network, largely in frontotemporoparietal regions. ROI analyses demonstrated significant effects (but no interactions) of task demand in the left and right inferior frontal gyrus, the left posterior middle temporal gyrus, the posterior inferior temporal gyrus and the prefrontal gyrus. Overall, our test did not confirm the CRUNCH predictions. [ABSTRACT FROM AUTHOR]

This paper evaluates data stream classifiers from the perspective of connected devices, focusing on the use case of Human Activity Recognition. We measure both the classification performance and resource consumption (runtime, memory, and power) of five usual stream classification algorithms, implemented in a consistent library, and applied to two real human activity datasets and three synthetic datasets. Regarding classification performance, the results show the overall superiority of the Hoeffding Tree, the Mondrian forest, and the Naïve Bayes classifiers over the Feedforward Neural Network and the Micro Cluster Nearest Neighbor classifiers on four datasets out of six, including the real ones. In addition, the Hoeffding Tree and—to some extent—the Micro Cluster Nearest Neighbor, are the only classifiers that can recover from a concept drift. Overall, the three leading classifiers still perform substantially worse than an offline classifier on the real datasets. Regarding resource consumption, the Hoeffding Tree and the Mondrian forest are the most memory intensive and have the longest runtime; however, no difference in power consumption is found between classifiers. We conclude that stream learning for Human Activity Recognition on connected objects is challenged by two factors which could lead to interesting future work: a high memory consumption and low F1 scores overall. [ABSTRACT FROM AUTHOR]

Context: An existing major challenge in Parkinson's disease (PD) research is the identification of biomarkers of disease progression. While magnetic resonance imaging is a potential source of PD biomarkers, none of the magnetic resonance imaging measures of PD are robust enough to warrant their adoption in clinical research. This study is part of a project that aims to replicate 11 PD studies reviewed in a recent survey (JAMA neurology, 78(10) 2021) to investigate the robustness of PD neuroimaging findings to data and analytical variations. Objective: This study attempts to replicate the results in Hanganu et al. (Brain, 137(4) 2014) using data from the Parkinson's Progression Markers Initiative (PPMI). Methods: Using 25 PD subjects and 18 healthy controls, we analyzed the rate of change of cortical thickness and of the volume of subcortical structures, and we measured the relationship between structural changes and cognitive decline. We compared our findings to the results in the original study. Results: (1) Similarly to the original study, PD patients with mild cognitive impairment (MCI) exhibited increased cortical thinning over time compared to patients without MCI in the right middle temporal gyrus, insula, and precuneus. (2) The rate of cortical thinning in the left inferior temporal and precentral gyri in PD patients correlated with the change in cognitive performance. (3) There were no group differences in the change of subcortical volumes. (4) We did not find a relationship between the change in subcortical volumes and the change in cognitive performance. Conclusion: Despite important differences in the dataset used in this replication study, and despite differences in sample size, we were able to partially replicate the original results. We produced a publicly available reproducible notebook allowing researchers to further investigate the reproducibility of the results in Hanganu et al. (2014) when more data is added to PPMI. [ABSTRACT FROM AUTHOR]

Convolutional neural networks (CNNs) are currently among the most widely-used deep neural network (DNN) architectures available and achieve state-of-the-art performance for many problems. Originally applied to computer vision tasks, CNNs work well with any data with a spatial relationship, besides images, and have been applied to different fields. However, recent works have highlighted numerical stability challenges in DNNs, which also relates to their known sensitivity to noise injection. These challenges can jeopardise their performance and reliability. This paper investigates DeepGOPlus, a CNN that predicts protein function. DeepGOPlus has achieved state-of-the-art performance and can successfully take advantage and annotate the abounding protein sequences emerging in proteomics. We determine the numerical stability of the model's inference stage by quantifying the numerical uncertainty resulting from perturbations of the underlying floating-point data. In addition, we explore the opportunity to use reduced-precision floating point formats for DeepGOPlus inference, to reduce memory consumption and latency. This is achieved by instrumenting DeepGOPlus' execution using Monte Carlo Arithmetic, a technique that experimentally quantifies floating point operation errors and VPREC, a tool that emulates results with customizable floating point precision formats. Focus is placed on the inference stage as it is the primary deliverable of the DeepGOPlus model, widely applicable across different environments. All in all, our results show that although the DeepGOPlus CNN is very stable numerically, it can only be selectively implemented with lower-precision floating-point formats. We conclude that predictions obtained from the pre-trained DeepGOPlus model are very reliable numerically, and use existing floating-point formats efficiently. [ABSTRACT FROM AUTHOR]

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science. [ABSTRACT FROM AUTHOR]

The analysis of brain-imaging data requires complex processing pipelines to support findings on brain function or pathologies. Recent work has shown that variability in analytical decisions, small amounts of noise, or computational environments can lead to substantial differences in the results, endangering the trust in conclusions. We explored the instability of results by instrumenting a structural connectome estimation pipeline with Monte Carlo Arithmetic to introduce random noise throughout. We evaluated the reliability of the connectomes, the robustness of their features, and the eventual impact on analysis. The stability of results was found to range from perfectly stable (i.e. all digits of data significant) to highly unstable (i.e. 0 − 1 significant digits). This paper highlights the potential of leveraging induced variance in estimates of brain connectivity to reduce the bias in networks without compromising reliability, alongside increasing the robustness and potential upper-bound of their applications in the classification of individual differences. We demonstrate that stability evaluations are necessary for understanding error inherent to brain imaging experiments, and how numerical analysis can be applied to typical analytical workflows both in brain imaging and other domains of computational sciences, as the techniques used were data and context agnostic and globally relevant. Overall, while the extreme variability in results due to analytical instabilities could severely hamper our understanding of brain organization, it also affords us the opportunity to increase the robustness of findings. [ABSTRACT FROM AUTHOR]

Neuroimaging stands to benefit from emerging ultrahigh-resolution 3D histological atlases of the human brain; the first of which is 'BigBrain'. Here, we review recent methodological advances for the integration of BigBrain with multi-modal neuroimaging and introduce a toolbox, 'BigBrainWarp', that combines these developments. The aim of BigBrainWarp is to simplify work-flows and support the adoption of best practices. This is accomplished with a simple wrapper function that allows users to easily map data between BigBrain and standard MRI spaces. The function automatically pulls specialised transformation procedures, based on ongoing research from a wide collaborative network of researchers. Additionally, the toolbox improves accessibility of histological information through dissemination of ready-to- use cytoarchitectural features. Finally, we demonstrate the utility of BigBrainWarp with three tutorials and discuss the potential of the toolbox to support multi-scale investigations of brain organisation. [ABSTRACT FROM AUTHOR]

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g. caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume. [ABSTRACT FROM AUTHOR]

Background Software containers greatly facilitate the deployment and reproducibility of scientific data analyses in various platforms. However, container images often contain outdated or unnecessary software packages, which increases the number of security vulnerabilities in the images, widens the attack surface in the container host, and creates substantial security risks for computing infrastructures at large. This article presents a vulnerability analysis of container images for scientific data analysis. We compare results obtained with 4 vulnerability scanners, focusing on the use case of neuroscience data analysis, and quantifying the effect of image update and minification on the number of vulnerabilities. Results We find that container images used for neuroscience data analysis contain hundreds of vulnerabilities, that software updates remove roughly two-thirds of these vulnerabilities, and that removing unused packages is also effective. Conclusions We provide recommendations on how to build container images with fewer vulnerabilities. [ABSTRACT FROM AUTHOR]

Background Data analysis pipelines are known to be affected by computational conditions, presumably owing to the creation and propagation of numerical errors. While this process could play a major role in the current reproducibility crisis, the precise causes of such instabilities and the path along which they propagate in pipelines are unclear. Method We present Spot, a tool to identify which processes in a pipeline create numerical differences when executed in different computational conditions. Spot leverages system-call interception through ReproZip to reconstruct and compare provenance graphs without pipeline instrumentation. Results By applying Spot to the structural pre-processing pipelines of the Human Connectome Project, we found that linear and non-linear registration are the cause of most numerical instabilities in these pipelines, which confirms previous findings. [ABSTRACT FROM AUTHOR]

With an increase in awareness regarding a troubling lack of reproducibility in analytical software tools, the degree of validity in scientific derivatives and their downstream results has become unclear. The nature of reproducibility issues may vary across domains, tools, data sets, and computational infrastructures, but numerical instabilities are thought to be a core contributor. In neuroimaging, unexpected deviations have been observed when varying operating systems, software implementations, or adding negligible quantities of noise. In the field of numerical analysis, these issues have recently been explored through Monte Carlo Arithmetic, a method involving the instrumentation of floating-point operations with probabilistic noise injections at a target precision. Exploring multiple simulations in this context allows the characterization of the result space for a given tool or operation. In this article, we compare various perturbation models to introduce instabilities within a typical neuroimaging pipeline, including (i) targeted noise, (ii) Monte Carlo Arithmetic, and (iii) operating system variation, to identify the significance and quality of their impact on the resulting derivatives. We demonstrate that even low-order models in neuroimaging such as the structural connectome estimation pipeline evaluated here are sensitive to numerical instabilities, suggesting that stability is a relevant axis upon which tools are compared, alongside more traditional criteria such as biological feasibility, computational efficiency, or, when possible, accuracy. Heterogeneity was observed across participants which clearly illustrates a strong interaction between the tool and data set being processed, requiring that the stability of a given tool be evaluated with respect to a given cohort. We identify use cases for each perturbation method tested, including quality assurance, pipeline error detection, and local sensitivity analysis, and make recommendations for the evaluation of stability in a practical and analytically focused setting. Identifying how these relationships and recommendations scale to higher order computational tools, distinct data sets, and their implication on biological feasibility remain exciting avenues for future work. [ABSTRACT FROM AUTHOR]

The sliding window technique is widely used to segment inertial sensor signals, i.e., accelerometers and gyroscopes, for activity recognition. In this technique, the sensor signals are partitioned into fix sized time windows which can be of two types: (1) non-overlapping windows, in which time windows do not intersect, and (2) overlapping windows, in which they do. There is a generalized idea about the positive impact of using overlapping sliding windows on the performance of recognition systems in Human Activity Recognition. In this paper, we analyze the impact of overlapping sliding windows on the performance of Human Activity Recognition systems with different evaluation techniques, namely, subject-dependent cross validation and subject-independent cross validation. Our results show that the performance improvements regarding overlapping windowing reported in the literature seem to be associated with the underlying limitations of subject-dependent cross validation. Furthermore, we do not observe any performance gain from the use of such technique in conjunction with subject-independent cross validation. We conclude that when using subject-independent cross validation, non-overlapping sliding windows reach the same performance as sliding windows. This result has significant implications on the resource usage for training the human activity recognition systems. [ABSTRACT FROM AUTHOR]

Introduction Automatic functional volume segmentation in PET images is a challenge that has been addressed using a large array of methods. A major limitation for the field has been the lack of a benchmark dataset that would allow direct comparison of the results in the various publications. In the present work, we describe a comparison of recent methods on a large dataset following recommendations by the American Association of Physicists in Medicine (AAPM) task group (TG) 211, which was carried out within a MICCAI (Medical Image Computing and Computer Assisted Intervention) challenge. Materials and methods Organization and funding was provided by France Life Imaging (FLI). A dataset of 176 images combining simulated, phantom and clinical images was assembled. A website allowed the participants to register and download training data (n = 19). Challengers then submitted encapsulated pipelines on an online platform that autonomously ran the algorithms on the testing data (n = 157) and evaluated the results. The methods were ranked according to the arithmetic mean of sensitivity and positive predictive value. Results Sixteen teams registered but only four provided manuscripts and pipeline(s) for a total of 10 methods. In addition, results using two thresholds and the Fuzzy Locally Adaptive Bayesian (FLAB) were generated. All competing methods except one performed with median accuracy above 0.8. The method with the highest score was the convolutional neural network-based segmentation, which significantly outperformed 9 out of 12 of the other methods, but not the improved K-Means, Gaussian Model Mixture and Fuzzy C-Means methods. Conclusion The most rigorous comparative study of PET segmentation algorithms to date was carried out using a dataset that is the largest used in such studies so far. The hierarchy amongst the methods in terms of accuracy did not depend strongly on the subset of datasets or the metrics (or combination of metrics). All the methods submitted by the challengers except one demonstrated good performance with median accuracy scores above 0.8. [ABSTRACT FROM AUTHOR]

Background and Purpose: The measurement of cortical shrinkage is a candidate marker of disease progression in Alzheimer’s. This study evaluated the performance of two pipelines: Civet-CLASP (v1.1.9) and Freesurfer (v5.3.0). Methods: Images from 185 ADNI1 cases (69 elderly controls (CTR), 37 stable MCI (sMCI), 27 progressive MCI (pMCI), and 52 Alzheimer (AD) patients) scanned at baseline, month 12, and month 24 were processed using the two pipelines and two interconnected e-infrastructures: neuGRID () and VIP (). The vertex-by-vertex cross-algorithm comparison was made possible applying the 3D gradient vector flow (GVF) and closest point search (CPS) techniques. Results: The cortical thickness measured with Freesurfer was systematically lower by one third if compared to Civet’s. Cross-sectionally, Freesurfer’s effect size was significantly different in the posterior division of the temporal fusiform cortex. Both pipelines were weakly or mildly correlated with the Mini Mental State Examination score (MMSE) and the hippocampal volumetry. Civet differed significantly from Freesurfer in large frontal, parietal, temporal and occipital regions (p<0.05). In a discriminant analysis with cortical ROIs having effect size larger than 0.8, both pipelines gave no significant differences in area under the curve (AUC). Longitudinally, effect sizes were not significantly different in any of the 28 ROIs tested. Both pipelines weakly correlated with MMSE decay, showing no significant differences. Freesurfer mildly correlated with hippocampal thinning rate and differed in the supramarginal gyrus, temporal gyrus, and in the lateral occipital cortex compared to Civet (p<0.05). In a discriminant analysis with ROIs having effect size larger than 0.6, both pipelines yielded no significant differences in the AUC. Conclusions: Civet appears slightly more sensitive to the typical AD atrophic pattern at the MCI stage, but both pipelines can accurately characterize the topography of cortical thinning at the dementia stage. [ABSTRACT FROM AUTHOR]

MRI plays a crucial role in multiple sclerosis diagnostic and patient follow-up. In particular, the delineation of T2-FLAIR hyperintense lesions is crucial although mostly performed manually - a tedious task. Many methods have thus been proposed to automate this task. However, sufficiently large datasets with a thorough expert manual segmentation are still lacking to evaluate these methods. We present a unique dataset for MS lesions segmentation evaluation. It consists of 53 patients acquired on 4 different scanners with a harmonized protocol. Hyperintense lesions on FLAIR were manually delineated on each patient by 7 experts with control on T2 sequence, and gathered in a consensus segmentation for evaluation. We provide raw and preprocessed data and a split of the dataset into training and testing data, the latter including data from a scanner not present in the training dataset. We strongly believe that this dataset will become a reference in MS lesions segmentation evaluation, allowing to evaluate many aspects: evaluation of performance on unseen scanner, comparison to individual experts performance, comparison to other challengers who already used this dataset, etc. [ABSTRACT FROM AUTHOR]

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-theart algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, …), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores. [ABSTRACT FROM AUTHOR]