brainlife.io: A decentralized and open source cloud platform to support neuroscience research

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR data analysis to portions of the worldwide research community. brainlife.io was developed to reduce these burdens and democratize modern neuroscience research across institutions and career levels. Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. brainlife.io automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here brainlife.io's technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility. Using data from 4 modalities and 3,200 participants, we demonstrate that brainlife.io's services produce outputs that adhere to best practices in modern neuroscience research

brainlife.io: a decentralized and open-source cloud platform to support neuroscience research

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants

Ensemble machine learning prediction of posttraumatic stress disorder screening status after emergency room hospitalization

Posttraumatic stress disorder (PTSD) develops in a substantial minority of emergency room admits. Inexpensive and accurate person-level assessment of PTSD risk after trauma exposure is a critical precursor to large-scale deployment of early interventions that may reduce individual suffering and societal costs. Toward this aim, we applied ensemble machine learning to predict PTSD status three months after severe injury using cost-effective and minimally invasive data. Participants (N = 271) were recruited at a Level 1 Trauma Center where they provided variables routinely collected at the hospital, including pulse, injury severity, and demographics, as well as psychological variables, including self-reported current depression, psychiatric history, and social support. Participant zip codes were used to extract contextual variables including population total and density, average annual income, and health insurance coverage rates from publicly available U.S. Census data. Machine learning yielded good prediction of PTSD status 3 months post-hospitalization, AUC = 0.85 95% CI [0.83, 0.86], and significantly outperformed all benchmark comparison models in a cross-validation procedure designed to yield an unbiased estimate of performance. These results demonstrate that good prediction can be attained from variables that individually have relatively weak predictive value, pointing to the promise of ensemble machine learning approaches that do not rely on strong isolated risk factors

Ensemble machine learning prediction of posttraumatic stress disorder screening status after emergency room hospitalization

Posttraumatic stress disorder (PTSD) develops in a substantial minority of emergency room admits. Inexpensive and accurate person-level assessment of PTSD risk after trauma exposure is a critical precursor to large-scale deployment of early interventions that may reduce individual suffering and societal costs. Toward this aim, we applied ensemble machine learning to predict PTSD status three months after severe injury using cost-effective and minimally invasive data. Participants (N = 271) were recruited at a Level 1 Trauma Center where they provided variables routinely collected at the hospital, including pulse, injury severity, and demographics, as well as psychological variables, including self-reported current depression, psychiatric history, and social support. Participant zip codes were used to extract contextual variables including population total and density, average annual income, and health insurance coverage rates from publicly available U.S. Census data. Machine learning yielded good prediction of PTSD status 3 months post-hospitalization, AUC = 0.85 95% CI [0.83, 0.86], and significantly outperformed all benchmark comparison models in a cross-validation procedure designed to yield an unbiased estimate of performance. These results demonstrate that good prediction can be attained from variables that individually have relatively weak predictive value, pointing to the promise of ensemble machine learning approaches that do not rely on strong isolated risk factors

Attentional bias modification treatment for depression: Study protocol for a randomized controlled trial

Theoretical models and empirical research point to negatively biased attention as a maintaining factor in depression. Although preliminary studies suggest experimentally modifying attentional biases (i.e., attentional bias modification; ABM) reduces depression symptoms and depression risk, relatively few rigorous studies with clinical samples have been completed. This clinical trial examines the impact of ABM on a sample of adults (N = 123) with elevated depression severity who also exhibit at least modest levels of negatively biased attention prior to treatment. Participants will be randomly assigned to either active ABM, placebo ABM, or an assessment-only control condition. Individuals assigned to ABM will complete 5 trainings per week (2 in-clinic, 3 brief trainings at-home) during a four-week period. Throughout this four-week period, participants will complete weekly assessments of symptom severity and putative treatment mediators measured across different levels of analysis (e.g., eye tracking, behavioral measures, and functional Magnetic Resonance Imaging). This article details the rationale and design of the clinical trial, including methodological issues that required more extensive consideration. Our findings may not only point to an easily-accessible, efficacious treatment for depression but may also provide a meaningful test of whether a theoretically important construct, negatively biased attention, maintains depression

Attentional bias modification treatment for depression: Study protocol for a randomized controlled trial

Theoretical models and empirical research point to negatively biased attention as a maintaining factor in depression. Although preliminary studies suggest experimentally modifying attentional biases (i.e., attentional bias modification; ABM) reduces depression symptoms and depression risk, relatively few rigorous studies with clinical samples have been completed. This clinical trial examines the impact of ABM on a sample of adults (N = 123) with elevated depression severity who also exhibit at least modest levels of negatively biased attention prior to treatment. Participants will be randomly assigned to either active ABM, placebo ABM, or an assessment-only control condition. Individuals assigned to ABM will complete 5 trainings per week (2 in-clinic, 3 brief trainings at-home) during a four-week period. Throughout this four-week period, participants will complete weekly assessments of symptom severity and putative treatment mediators measured across different levels of analysis (e.g., eye tracking, behavioral measures, and functional Magnetic Resonance Imaging). This article details the rationale and design of the clinical trial, including methodological issues that required more extensive consideration. Our findings may not only point to an easily-accessible, efficacious treatment for depression but may also provide a meaningful test of whether a theoretically important construct, negatively biased attention, maintains depression

brainlife.io: a decentralized and open-source cloud platform to support neuroscience research

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.</p

nilearn

Nilearn enables approachable and versatile analyses of brain volumes. It provides statistical and machine-learning tools, with instructive documentation &amp; friendly community.If you use this software, please cite it as below