Open and reproducible neuroimaging: From study inception to publication

Rethinking MRI as a measurement device through modular and portable pipelines

The premise of MRI as a reliable measurement device is limited by proprietary barriers and inconsistent implementations, which prevent the establishment of measurement uncertainties. As a result, biomedical studies that rely on these methods are plagued by systematic variance, undermining the perceived promise of quantitative imaging biomarkers (QIBs) and hindering their clinical translation. This review explores the added value of open-source measurement pipelines in minimizing variability sources that would otherwise remain unknown. First, we introduce a tiered benchmarking framework (from black-box to glass-box) that exposes how opacity at different workflow stages propagates measurement uncertainty. Second, we provide a concise glossary to promote consistent terminology for strategies that enhance reproducibility before acquisition or enable valid post-hoc pooling of QIBs. Building on this foundation, we present two illustrative measurement workflows that decouple workflow logic from the orchestration of computational processes in an MRI measurement pipeline, rooted in the core principles of modularity and portability. Designed as accessible entry points for implementation, these examples serve as practical guides, helping users adapt the frameworks to their specific needs and facilitating collaboration. Through critical evaluation of existing approaches, we discuss how standardized workflows can help identify outstanding challenges in translating glass-box frameworks into clinical scanner environments. Ultimately, achieving this goal will require coordinated efforts from QIB developers, regulators, industry partners, and clinicians alike.

Ten principles for reliable, efficient, and adaptable coding in psychology and cognitive neuroscience

Writing code is becoming essential for psychology and neuroscience research, supporting increasingly advanced experimental designs, processing of ever-larger datasets and easy reproduction of scientific results. Despite its critical role, coding remains challenging for many researchers, as it is typically not part of formal academic training. We present a range of practices tailored to different levels of programming experience, from beginners to advanced users. Our ten principles help researchers streamline and automate their projects, reduce human error, and improve the quality and reusability of their code. For principal investigators, we highlight the benefits of fostering a collaborative environment that values code sharing. Maintaining basic standards for code quality, reusability, and shareability is critical for increasing the trustworthiness and reliability of research in experimental psychology and cognitive neuroscience.

How will developmental neuroimaging contribute to the prediction of neurodevelopmental or psychiatric disorders? Challenges and opportunities

Successful developmental neuroimaging efforts require interdisciplinary expertise to ground scientific questions in knowledge of human development, modify and create technologies and data processing pipelines suited to the young brain, and ensure research procedures meet the needs and protect the interests of young children and their caregivers. This paper brings together four interdisciplinary perspectives to tackle a set of questions that are central for the field to address as we imagine a future role for developmental neuroimaging in the prediction of neurodevelopmental or psychiatric disorders: 1) How do we generate a strong evidence base for causality and clinical relevance? 2) How do we ensure the integrity of the data and support fair and wide access? 3) How can these technologies be implemented in the clinic? 4) What are the ethical obligations for neuroimaging researchers working with infants and young children?

From lab to life: challenges and perspectives of fNIRS for haemodynamic-based neurofeedback in real-world environments

Neurofeedback allows individuals to monitor and self-regulate their brain activity, potentially improving human brain function. Beyond the traditional electrophysiological approach using primarily electroencephalography, brain haemodynamics measured with functional magnetic resonance imaging (fMRI) and more recently, functional near-infrared spectroscopy (fNIRS) have been used (haemodynamic-based neurofeedback), particularly to improve the spatial specificity of neurofeedback. Over recent years, especially fNIRS has attracted great attention because it offers several advantages over fMRI such as increased user accessibility, cost-effectiveness and mobility-the latter being the most distinct feature of fNIRS. The next logical step would be to transfer haemodynamic-based neurofeedback protocols that have already been proven and validated by fMRI to mobile fNIRS. However, this undertaking is not always easy, especially since fNIRS novices may miss important fNIRS-specific methodological challenges. This review is aimed at researchers from different fields who seek to exploit the unique capabilities of fNIRS for neurofeedback. It carefully addresses fNIRS-specific challenges and offers suggestions for possible solutions. If the challenges raised are addressed and further developed, fNIRS could emerge as a useful neurofeedback technique with its own unique application potential-the targeted training of brain activity in real-world environments, thereby significantly expanding the scope and scalability of haemodynamic-based neurofeedback applications.This article is part of the theme issue 'Neurofeedback: new territories and neurocognitive mechanisms of endogenous neuromodulation'.

Constructing and exploring neuroimaging projects: a survey from clinical practice to scientific research

Over the past decades, numerous large-scale neuroimaging projects that involved the collection and release of multimodal data have been conducted globally. Distinguished initiatives such as the Human Connectome Project, UK Biobank, and Alzheimer's Disease Neuroimaging Initiative, among others, stand as remarkable international collaborations that have significantly advanced our understanding of the brain. With the advancement of big data technology, changes in healthcare models, and continuous development in biomedical research, various types of large-scale projects are being established and promoted worldwide. For project leaders, there is a need to refer to common principles in project construction and management. Users must also adhere strictly to rules and guidelines, ensuring data safety and privacy protection. Organizations must maintain data integrity, protect individual privacy, and foster stakeholders' trust. Regular updates to legislation and policies are necessary to keep pace with evolving technologies and emerging data-related challenges. CRITICAL RELEVANCE STATEMENT: By reviewing global large-scale neuroimaging projects, we have summarized the standards and norms for establishing and utilizing their data, and provided suggestions and opinions on some ethical issues, aiming to promote higher-quality neuroimaging data development. KEY POINTS: Global neuroimaging projects are increasingly advancing but still face challenges. Constructing and utilizing neuroimaging projects should follow set rules and guidelines. Effective data management and governance should be developed to support neuroimaging projects.

ComBat models for harmonization of resting-state EEG features in multisite studies

OBJECTIVE

Pooling multisite resting-state electroencephalography (rsEEG) datasets may introduce bias due to batch effects (i.e., cross-site differences in the rsEEG related to scanner/sample characteristics). The Combining Batches (ComBat) models, introduced for microarray expression and adapted for neuroimaging, can control for batch effects while preserving the variability of biological covariates. We aim to evaluate four ComBat harmonization methods in a pooled sample from five independent rsEEG datasets of young and old adults.

METHODS

RsEEG signals (n = 374) were automatically preprocessed. Oscillatory and aperiodic rsEEG features were extracted in sensor space. Features were harmonized using neuroCombat (standard ComBat used in neuroimaging), neuroHarmonize (variant with nonlinear adjustment of covariates), OPNested-GMM (variant based on Gaussian Mixture Models to fit bimodal feature distributions), and HarmonizR (variant based on resampling to handle missing feature values). Relationships between rsEEG features and age were explored before and after harmonizing batch effects.

RESULTS

Batch effects were identified in rsEEG features. All ComBat methods reduced batch effects and features' dispersion; HarmonizR and OPNested-GMM ComBat achieved the greatest performance. Harmonized Beta power, individual Alpha peak frequency, Aperiodic exponent, and offset in posterior electrodes showed significant relations with age. All ComBat models maintained the direction of observed relationships while increasing the effect size.

CONCLUSIONS

ComBat models, particularly HarmonizeR and OPNested-GMM ComBat, effectively control for batch effects in rsEEG spectral features.

SIGNIFICANCE

This workflow can be used in multisite studies to harmonize batch effects in sensor-space rsEEG spectral features while preserving biological associations.

Quality assessment and control of unprocessed anatomical, functional, and diffusion MRI of the human brain using MRIQC

Quality control of MRI data prior to preprocessing is fundamental, as substandard data are known to increase variability spuriously. Currently, no automated or manual method reliably identifies subpar images, given pre-specified exclusion criteria. In this work, we propose a protocol describing how to carry out the visual assessment of T1-weighted, T2-weighted, functional, and diffusion MRI scans of the human brain with the visual reports generated by MRIQC. The protocol describes how to execute the software on all the images of the input dataset using typical research settings (i.e., a high-performance computing cluster). We then describe how to screen the visual reports generated with MRIQC to identify artifacts and potential quality issues and annotate the latter with the "rating widget" ─ a utility that enables rapid annotation and minimizes bookkeeping errors. Integrating proper quality control checks on the unprocessed data is fundamental to producing reliable statistical results and crucial to identifying faults in the scanning settings, preempting the acquisition of large datasets with persistent artifacts that should have been addressed as they emerged.

FetMRQC: A robust quality control system for multi-centric fetal brain MRI

Fetal brain MRI is becoming an increasingly relevant complement to neurosonography for perinatal diagnosis, allowing fundamental insights into fetal brain development throughout gestation. However, uncontrolled fetal motion and heterogeneity in acquisition protocols lead to data of variable quality, potentially biasing the outcome of subsequent studies. We present FetMRQC, an open-source machine-learning framework for automated image quality assessment and quality control that is robust to domain shifts induced by the heterogeneity of clinical data. FetMRQC extracts an ensemble of quality metrics from unprocessed anatomical MRI and combines them to predict experts' ratings using random forests. We validate our framework on a pioneeringly large and diverse dataset of more than 1600 manually rated fetal brain T2-weighted images from four clinical centers and 13 different scanners. Our study shows that FetMRQC's predictions generalize well to unseen data while being interpretable. FetMRQC is a step towards more robust fetal brain neuroimaging, which has the potential to shed new insights on the developing human brain.

Resting-state electroencephalography and magnetoencephalography in migraine-a systematic review and meta-analysis

Magnetoencephalography/electroencephalography (M/EEG) can provide insights into migraine pathophysiology and help develop clinically valuable biomarkers. To integrate and summarize the existing evidence on changes in brain function in migraine, we performed a systematic review and meta-analysis (PROSPERO CRD42021272622) of resting-state M/EEG findings in migraine. We included 27 studies after searching MEDLINE, Web of Science Core Collection, and EMBASE. Risk of bias was assessed using a modified Newcastle-Ottawa Scale. Semi-quantitative analysis was conducted by vote counting, and meta-analyses of M/EEG differences between people with migraine and healthy participants were performed using random-effects models. In people with migraine during the interictal phase, meta-analysis revealed higher power of brain activity at theta frequencies (3-8 Hz) than in healthy participants. Furthermore, we found evidence for lower alpha and beta connectivity in people with migraine in the interictal phase. No associations between M/EEG features and disease severity were observed. Moreover, some evidence for higher delta and beta power in the premonitory compared to the interictal phase was found. Strongest risk of bias of included studies arose from a lack of controlling for comorbidities and non-automatized or non-blinded M/EEG assessments. These findings can guide future M/EEG studies on migraine pathophysiology and brain-based biomarkers, which should consider comorbidities and aim for standardized, collaborative approaches.

Reproducible Research Practices in Magnetic Resonance Neuroimaging: A Review Informed by Advanced Language Models

MRI has progressed significantly with the introduction of advanced computational methods and novel imaging techniques, but their wider adoption hinges on their reproducibility. This concise review synthesizes reproducible research insights from recent MRI articles to examine the current state of reproducibility in neuroimaging, highlighting key trends and challenges. It also provides a custom generative pretrained transformer (GPT) model, designed specifically for aiding in an automated analysis and synthesis of information pertaining to the reproducibility insights associated with the articles at the core of this review.

MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology

Magnetic resonance imaging of the brain is a useful tool in both the clinic and research settings, aiding in the diagnosis and treatments of neurological disease and expanding our knowledge of the brain. However, there are many challenges inherent in managing and analyzing MRI data, due in large part to the heterogeneity of data acquisition. To address this, we have developed MRIO, the Magnetic Resonance Imaging Acquisition and Analysis Ontology. MRIO provides well-reasoned classes and logical axioms for the acquisition of several MRI acquisition types and well-known, peer-reviewed analysis software, facilitating the use of MRI data. These classes provide a common language for the neuroimaging research process and help standardize the organization and analysis of MRI data for reproducible datasets. We also provide queries for automated assignment of analyses for given MRI types. MRIO aids researchers in managing neuroimaging studies by helping organize and annotate MRI data and integrating with existing standards such as Digital Imaging and Communications in Medicine and the Brain Imaging Data Structure, enhancing reproducibility and interoperability. MRIO was constructed according to Open Biomedical Ontologies Foundry principles and has contributed several classes to the Ontology for Biomedical Investigations to help bridge neuroimaging data to other domains. MRIO addresses the need for a "common language" for MRI that can help manage the neuroimaging research, by enabling researchers to identify appropriate analyses for sets of scans and facilitating data organization and reporting.

Open-source magnetic resonance imaging: Improving access, science, and education through global collaboration

Open-source practices and resources in magnetic resonance imaging (MRI) have increased substantially in recent years. This trend started with software and data being published open-source and, more recently, open-source hardware designs have become increasingly available. These developments towards a culture of sharing and establishing nonexclusive global collaborations have already improved the reproducibility and reusability of code and designs, while providing a more inclusive approach, especially for low-income settings. Community-driven standardization and documentation efforts are further strengthening and expanding these milestones. The future of open-source MRI is bright and we have just started to discover its full collaborative potential. In this review we will give an overview of open-source software and open-source hardware projects in human MRI research.

The Advanced BRain Imaging on ageing and Memory (ABRIM) data collection: Study design, data processing, and rationale

To understand the neurocognitive mechanisms that underlie heterogeneity in cognitive ageing, recent scientific efforts have led to a growing public availability of imaging cohort data. The Advanced BRain Imaging on ageing and Memory (ABRIM) project aims to add to these existing datasets by taking an adult lifespan approach to provide a cross-sectional, normative database with a particular focus on connectivity, myelinization and iron content of the brain in concurrence with cognitive functioning, mechanisms of reserve, and sleep-wake rhythms. ABRIM freely shares MRI and behavioural data from 295 participants between 18-80 years, stratified by age decade and sex (median age 52, IQR 36-66, 53.20% females). The ABRIM MRI collection consists of both the raw and pre-processed structural and functional MRI data to facilitate data usage among both expert and non-expert users. The ABRIM behavioural collection includes measures of cognitive functioning (i.e., global cognition, processing speed, executive functions, and memory), proxy measures of cognitive reserve (e.g., educational attainment, verbal intelligence, and occupational complexity), and various self-reported questionnaires (e.g., on depressive symptoms, pain, and the use of memory strategies in daily life and during a memory task). In a sub-sample (n = 120), we recorded sleep-wake rhythms using an actigraphy device (Actiwatch 2, Philips Respironics) for a period of 7 consecutive days. Here, we provide an in-depth description of our study protocol, pre-processing pipelines, and data availability. ABRIM provides a cross-sectional database on healthy participants throughout the adult lifespan, including numerous parameters relevant to improve our understanding of cognitive ageing. Therefore, ABRIM enables researchers to model the advanced imaging parameters and cognitive topologies as a function of age, identify the normal range of values of such parameters, and to further investigate the diverse mechanisms of reserve and resilience.

The power of many brains: Catalyzing neuropsychiatric discovery through open neuroimaging data and large-scale collaboration

Recent advances in open neuroimaging data are enhancing our comprehension of neuropsychiatric disorders. By pooling images from various cohorts, statistical power has increased, enabling the detection of subtle abnormalities and robust associations, and fostering new research methods. Global collaborations in imaging have furthered our knowledge of the neurobiological foundations of brain disorders and aided in imaging-based prediction for more targeted treatment. Large-scale magnetic resonance imaging initiatives are driving innovation in analytics and supporting generalizable psychiatric studies. We also emphasize the significant role of big data in understanding neural mechanisms and in the early identification and precise treatment of neuropsychiatric disorders. However, challenges such as data harmonization across different sites, privacy protection, and effective data sharing must be addressed. With proper governance and open science practices, we conclude with a projection of how large-scale imaging resources and collaborations could revolutionize diagnosis, treatment selection, and outcome prediction, contributing to optimal brain health.

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

Neuroimaging research requires purpose-built analysis software, which is challenging to install and may produce different results across computing environments. The community-oriented, open-source Neurodesk platform ( https://www.neurodesk.org/ ) harnesses a comprehensive and growing suite of neuroimaging software containers. Neurodesk includes a browser-accessible virtual desktop, command-line interface and computational notebook compatibility, allowing for accessible, flexible, portable and fully reproducible neuroimaging analysis on personal workstations, high-performance computers and the cloud.

Interpersonal neural synchrony and mental disorders: unlocking potential pathways for clinical interventions

Introduction

Interpersonal synchronization involves the alignment of behavioral, affective, physiological, and brain states during social interactions. It facilitates empathy, emotion regulation, and prosocial commitment. Mental disorders characterized by social interaction dysfunction, such as Autism Spectrum Disorder (ASD), Reactive Attachment Disorder (RAD), and Social Anxiety Disorder (SAD), often exhibit atypical synchronization with others across multiple levels. With the introduction of the "second-person" neuroscience perspective, our understanding of interpersonal neural synchronization (INS) has improved, however, so far, it has hardly impacted the development of novel therapeutic interventions.

Methods

To evaluate the potential of INS-based treatments for mental disorders, we performed two systematic literature searches identifying studies that directly target INS through neurofeedback (12 publications; 9 independent studies) or brain stimulation techniques (7 studies), following PRISMA guidelines. In addition, we narratively review indirect INS manipulations through behavioral, biofeedback, or hormonal interventions. We discuss the potential of such treatments for ASD, RAD, and SAD and using a systematic database search assess the acceptability of neurofeedback (4 studies) and neurostimulation (4 studies) in patients with social dysfunction.

Results

Although behavioral approaches, such as engaging in eye contact or cooperative actions, have been shown to be associated with increased INS, little is known about potential long-term consequences of such interventions. Few proof-of-concept studies have utilized brain stimulation techniques, like transcranial direct current stimulation or INS-based neurofeedback, showing feasibility and preliminary evidence that such interventions can boost behavioral synchrony and social connectedness. Yet, optimal brain stimulation protocols and neurofeedback parameters are still undefined. For ASD, RAD, or SAD, so far no randomized controlled trial has proven the efficacy of direct INS-based intervention techniques, although in general brain stimulation and neurofeedback methods seem to be well accepted in these patient groups.

Discussion

Significant work remains to translate INS-based manipulations into effective treatments for social interaction disorders. Future research should focus on mechanistic insights into INS, technological advancements, and rigorous design standards. Furthermore, it will be key to compare interventions directly targeting INS to those targeting other modalities of synchrony as well as to define optimal target dyads and target synchrony states in clinical interventions.

Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn

Reducing contributions from non-neuronal sources is a crucial step in functional magnetic resonance imaging (fMRI) connectivity analyses. Many viable strategies for denoising fMRI are used in the literature, and practitioners rely on denoising benchmarks for guidance in the selection of an appropriate choice for their study. However, fMRI denoising software is an ever-evolving field, and the benchmarks can quickly become obsolete as the techniques or implementations change. In this work, we present a denoising benchmark featuring a range of denoising strategies, datasets and evaluation metrics for connectivity analyses, based on the popular fMRIprep software. The benchmark prototypes an implementation of a reproducible framework, where the provided Jupyter Book enables readers to reproduce or modify the figures on the Neurolibre reproducible preprint server (https://neurolibre.org/). We demonstrate how such a reproducible benchmark can be used for continuous evaluation of research software, by comparing two versions of the fMRIprep. Most of the benchmark results were consistent with prior literature. Scrubbing, a technique which excludes time points with excessive motion, combined with global signal regression, is generally effective at noise removal. Scrubbing was generally effective, but is incompatible with statistical analyses requiring the continuous sampling of brain signal, for which a simpler strategy, using motion parameters, average activity in select brain compartments, and global signal regression, is preferred. Importantly, we found that certain denoising strategies behave inconsistently across datasets and/or versions of fMRIPrep, or had a different behavior than in previously published benchmarks. This work will hopefully provide useful guidelines for the fMRIprep users community, and highlight the importance of continuous evaluation of research methods.

Testing the sensitivity of diagnosis-derived patterns in functional brain networks to symptom burden in a Norwegian youth sample

Aberrant brain network development represents a putative aetiological component in mental disorders, which typically emerge during childhood and adolescence. Previous studies have identified resting-state functional connectivity (RSFC) patterns reflecting psychopathology, but the generalisability to other samples and politico-cultural contexts has not been established. We investigated whether a previously identified cross-diagnostic case-control and autism spectrum disorder (ASD)-specific pattern of RSFC (discovery sample; aged 5-21 from New York City, USA; n = 1666) could be validated in a Norwegian convenience-based youth sample (validation sample; aged 9-25 from Oslo, Norway; n = 531). As a test of generalisability, we investigated if these diagnosis-derived RSFC patterns were sensitive to levels of symptom burden in both samples, based on an independent measure of symptom burden. Both the cross-diagnostic and ASD-specific RSFC pattern were validated across samples. Connectivity patterns were significantly associated with thematically appropriate symptom dimensions in the discovery sample. In the validation sample, the ASD-specific RSFC pattern showed a weak, inverse relationship with symptoms of conduct problems, hyperactivity and prosociality, while the cross-diagnostic pattern was not significantly linked to symptoms. Diagnosis-derived connectivity patterns in a developmental clinical US sample were validated in a convenience sample of Norwegian youth, however, they were not associated with mental health symptoms.

Brain health measurement: a scoping review

OBJECTIVES

Preservation of brain health is an urgent priority for the world's ageing population. The evidence base for brain health optimisation strategies is rapidly expanding, but clear recommendations have been limited by heterogeneity in measurement of brain health outcomes. We performed a scoping review to systematically evaluate brain health measurement in the scientific literature to date, informing development of a core outcome set.

DESIGN

Scoping review.

DATA SOURCES

Medline, APA PsycArticles and Embase were searched through until 25 January 2023.

ELIGIBILITY CRITERIA FOR SELECTING STUDIES

Studies were included if they described brain health evaluation methods in sufficient detail in human adults and were in English language.

DATA EXTRACTION AND SYNTHESIS

Two reviewers independently screened titles, abstracts and full texts for inclusion and extracted data using Covidence software.

RESULTS

From 6987 articles identified by the search, 727 studies met inclusion criteria. Study publication increased by 22 times in the last decade. Cohort study was the most common study design (n=609, 84%). 479 unique methods of measuring brain health were identified, comprising imaging, cognitive, mental health, biological and clinical categories. Seven of the top 10 most frequently used brain health measurement methods were imaging based, including structural imaging of grey matter and hippocampal volumes and white matter hyperintensities. Cognitive tests such as the trail making test accounted for 286 (59.7%) of all brain health measurement methods.

CONCLUSIONS

The scientific literature surrounding brain health has increased exponentially, yet measurement methods are highly heterogeneous across studies which may explain the lack of clinical translation. Future studies should aim to develop a selected group of measures that should be included in all brain health studies to aid interstudy comparison (core outcome set), and broaden from the current focus on neuroimaging outcomes to include a range of outcomes.

Cerebral MRI in a prospective cohort study on depression and atherosclerosis: the BiDirect sample, processing pipelines, and analysis tools

BACKGROUND

The use of cerebral magnetic resonance imaging (MRI) in observational studies has increased exponentially in recent years, making it critical to provide details about the study sample, image processing, and extracted imaging markers to validate and replicate study results. This article reviews the cerebral MRI dataset from the now-completed BiDirect cohort study, as an update and extension of the feasibility report published after the first two examination time points.

METHODS

We report the sample and flow of participants spanning four study sessions and twelve years. In addition, we provide details on the acquisition protocol; the processing pipelines, including standardization and quality control methods; and the analytical tools used and markers available.

RESULTS

All data were collected from 2010 to 2021 at a single site in Münster, Germany, starting with a population of 2,257 participants at baseline in 3 different cohorts: a population-based cohort (n = 911 at baseline, 672 with MRI data), patients diagnosed with depression (n = 999, 736 with MRI data), and patients with manifest cardiovascular disease (n = 347, 52 with MRI data). During the study period, a total of 4,315 MRI sessions were performed, and over 535 participants underwent MRI at all 4 time points.

CONCLUSIONS

Images were converted to Brain Imaging Data Structure (a standard for organizing and describing neuroimaging data) and analyzed using common tools, such as CAT12, FSL, Freesurfer, and BIANCA to extract imaging biomarkers. The BiDirect study comprises a thoroughly phenotyped study population with structural and functional MRI data.

RELEVANCE STATEMENT

The BiDirect Study includes a population-based sample and two patient-based samples whose MRI data can help answer numerous neuropsychiatric and cardiovascular research questions.

KEY POINTS

• The BiDirect study included characterized patient- and population-based cohorts with MRI data. • Data were standardized to Brain Imaging Data Structure and processed with commonly available software. • MRI data and markers are available upon request.

Opinion: Which animals have personality?

Human personality generally refers to coherent individuating patterns in affect, behavior, and cognition. We can only observe and measure behavior, from which we then infer personality and other psychological processes (affect, cognition, etc.). We emphasize that the study of personality always explains or summarizes patterns not only in behavior but also in these other psychological processes inferred from behavior. We thus argue that personality should be attributed only to nonhuman animals with behaviors from which we can infer a sufficiently rich set of psychological processes. The mere inference of a biological trait that explains behavioral variability, on our view, is not sufficient to count as a personality construct and should be given a different term. Methodologically, inferring personality in nonhuman animals entails challenges in characterizing ecologically valid behaviors, doing so across rich and varied environments, and collecting enough data. We suggest that studies should gradually accumulate such corpora of data on a species through well-curated shared databases. A mixture of approaches should include both top-down fit with extant human personality theories (such as the Big Five) as well as bottom-up discovery of species-specific personality dimensions. Adopting the above framework will help us to build a comparative psychology and will provide the most informative models also for understanding human personality, its evolution, and its disorders.

Functional magnetic resonance imaging in schizophrenia: current evidence, methodological advances, limitations and future directions

Functional neuroimaging emerged with great promise and has provided fundamental insights into the neurobiology of schizophrenia. However, it has faced challenges and criticisms, most notably a lack of clinical translation. This paper provides a comprehensive review and critical summary of the literature on functional neuroimaging, in particular functional magnetic resonance imaging (fMRI), in schizophrenia. We begin by reviewing research on fMRI biomarkers in schizophrenia and the clinical high risk phase through a historical lens, moving from case-control regional brain activation to global connectivity and advanced analytical approaches, and more recent machine learning algorithms to identify predictive neuroimaging features. Findings from fMRI studies of negative symptoms as well as of neurocognitive and social cognitive deficits are then reviewed. Functional neural markers of these symptoms and deficits may represent promising treatment targets in schizophrenia. Next, we summarize fMRI research related to antipsychotic medication, psychotherapy and psychosocial interventions, and neurostimulation, including treatment response and resistance, therapeutic mechanisms, and treatment targeting. We also review the utility of fMRI and data-driven approaches to dissect the heterogeneity of schizophrenia, moving beyond case-control comparisons, as well as methodological considerations and advances, including consortia and precision fMRI. Lastly, limitations and future directions of research in the field are discussed. Our comprehensive review suggests that, in order for fMRI to be clinically useful in the care of patients with schizophrenia, research should address potentially actionable clinical decisions that are routine in schizophrenia treatment, such as which antipsychotic should be prescribed or whether a given patient is likely to have persistent functional impairment. The potential clinical utility of fMRI is influenced by and must be weighed against cost and accessibility factors. Future evaluations of the utility of fMRI in prognostic and treatment response studies may consider including a health economics analysis.

Ideography insight from facial recognition and neuroimaging

One novel example and/or perspective in support of "Why the learning account fails" is the impressive ability of humans to recognize and memorize facial features and accurately and reliably connect those to related identities. Furthermore, neuroimaging analysis presents an example in support of the crucial role of standardization in the lack of adoption of ideography.

DISCOVER-EEG: an open, fully automated EEG pipeline for biomarker discovery in clinical neuroscience

Biomarker discovery in neurological and psychiatric disorders critically depends on reproducible and transparent methods applied to large-scale datasets. Electroencephalography (EEG) is a promising tool for identifying biomarkers. However, recording, preprocessing, and analysis of EEG data is time-consuming and researcher-dependent. Therefore, we developed DISCOVER-EEG, an open and fully automated pipeline that enables easy and fast preprocessing, analysis, and visualization of resting state EEG data. Data in the Brain Imaging Data Structure (BIDS) standard are automatically preprocessed, and physiologically meaningful features of brain function (including oscillatory power, connectivity, and network characteristics) are extracted and visualized using two open-source and widely used Matlab toolboxes (EEGLAB and FieldTrip). We tested the pipeline in two large, openly available datasets containing EEG recordings of healthy participants and patients with a psychiatric condition. Additionally, we performed an exploratory analysis that could inspire the development of biomarkers for healthy aging. Thus, the DISCOVER-EEG pipeline facilitates the aggregation, reuse, and analysis of large EEG datasets, promoting open and reproducible research on brain function.

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.

MRIO: The Magnetic Resonance Imaging Acquisition and Analysis Ontology

Objective

Magnetic resonance imaging of the brain is a useful tool in both the clinic and research settings, aiding in the diagnosis and treatments of neurological disease and expanding our knowledge of the brain. However, there are many challenges inherent in managing and analyzing MRI data, due in large part to the heterogeneity of data acquisition.

Materials and Methods

To address this, we have developed MRIO, the Magnetic Resonance Imaging Acquisition and Analysis Ontology.

Results

MRIO provides well-reasoned classes and logical axioms for the acquisition of several MRI acquisition types and well-known, peer-reviewed analysis software, facilitating the use of MRI data. These classes provide a common language for the neuroimaging research process and help standardize the organization and analysis of MRI data for reproducible datasets. We also provide queries for automated assignment of analyses for given MRI types.

Discussion

MRIO aids researchers in managing neuroimaging studies by helping organize and annotate MRI data and integrating with existing standards such as Digital Imaging and Communications in Medicine and the Brain Imaging Data Structure, enhancing reproducibility and interoperability. MRIO was constructed according to Open Biomedical Ontologies Foundry principals and has contributed several terms to the Ontology for Biomedical Investigations to help bridge neuroimaging data to other domains.

Conclusion

MRIO addresses the need for a "common language" for MRI that can help manage the neuroimaging research, by enabling researchers to identify appropriate analyses for sets of scans and facilitating data organization and reporting.

NIDM-Terms: community-based terminology management for improved neuroimaging dataset descriptions and query

The biomedical research community is motivated to share and reuse data from studies and projects by funding agencies and publishers. Effectively combining and reusing neuroimaging data from publicly available datasets, requires the capability to query across datasets in order to identify cohorts that match both neuroimaging and clinical/behavioral data criteria. Critical barriers to operationalizing such queries include, in part, the broad use of undefined study variables with limited or no annotations that make it difficult to understand the data available without significant interaction with the original authors. Using the Brain Imaging Data Structure (BIDS) to organize neuroimaging data has made querying across studies for specific image types possible at scale. However, in BIDS, beyond file naming and tightly controlled imaging directory structures, there are very few constraints on ancillary variable naming/meaning or experiment-specific metadata. In this work, we present NIDM-Terms, a set of user-friendly terminology management tools and associated software to better manage individual lab terminologies and help with annotating BIDS datasets. Using these tools to annotate BIDS data with a Neuroimaging Data Model (NIDM) semantic web representation, enables queries across datasets to identify cohorts with specific neuroimaging and clinical/behavioral measurements. This manuscript describes the overall informatics structures and demonstrates the use of tools to annotate BIDS datasets to perform integrated cross-cohort queries.

Continuous Evaluation of Denoising Strategies in Resting-State fMRI Connectivity Using fMRIPrep and Nilearn

Reducing contributions from non-neuronal sources is a crucial step in functional magnetic resonance imaging (fMRI) connectivity analyses. Many viable strategies for denoising fMRI are used in the literature, and practitioners rely on denoising benchmarks for guidance in the selection of an appropriate choice for their study. However, fMRI denoising software is an ever-evolving field, and the benchmarks can quickly become obsolete as the techniques or implementations change. In this work, we present a denoising benchmark featuring a range of denoising strategies, datasets and evaluation metrics for connectivity analyses, based on the popular fMRIprep software. The benchmark is implemented in a fully reproducible framework, where the provided research objects enable readers to reproduce or modify core computations, as well as the figures of the article using the Jupyter Book project and the Neurolibre reproducible preprint server (https://neurolibre.org/). We demonstrate how such a reproducible benchmark can be used for continuous evaluation of research software, by comparing two versions of the fMRIprep software package. The majority of benchmark results were consistent with prior literature. Scrubbing, a technique which excludes time points with excessive motion, combined with global signal regression, is generally effective at noise removal. Scrubbing however disrupts the continuous sampling of brain images and is incompatible with some statistical analyses, e.g. auto-regressive modeling. In this case, a simple strategy using motion parameters, average activity in select brain compartments, and global signal regression should be preferred. Importantly, we found that certain denoising strategies behave inconsistently across datasets and/or versions of fMRIPrep, or had a different behavior than in previously published benchmarks. This work will hopefully provide useful guidelines for the fMRIprep users community, and highlight the importance of continuous evaluation of research methods. Our reproducible benchmark infrastructure will facilitate such continuous evaluation in the future, and may also be applied broadly to different tools or even research fields.

Multiverse analyses of fear acquisition and extinction retention in posttraumatic stress disorder

Persistent fear is a cardinal feature of posttraumatic stress disorder (PTSD), and deficient fear extinction retention is a proposed illness mechanism and target of exposure-based therapy. However, evidence for deficient fear extinction in PTSD has been mixed using laboratory paradigms, which may relate to underidentified methodological variation across studies. We reviewed the literature to identify parameters that differ across studies of fear extinction retention in PTSD. We then performed Multiverse Analysis in a new sample, to quantify the impact of those methodological parameters on statistical findings. In 25 PTSD patients (15 female) and 36 trauma-exposed non-PTSD controls (TENC) (20 female), we recorded skin conductance response (SCR) during fear acquisition and extinction learning (day 1) and extinction recall (day 2). A first Multiverse Analysis examined the effects of methodological parameters identified by the literature review on comparisons of SCR-based fear extinction retention in PTSD versus TENC. A second Multiverse Analysis examined the effects of those methodological parameters on comparisons of SCR to a danger cue (CS+) versus safety cue (CS-) during fear acquisition. Both the literature review and the Multiverse Analysis yielded inconsistent findings for fear extinction retention in PTSD versus TENC, and most analyses found no statistically significant group difference. By contrast, significantly elevated SCR to CS+ versus CS- was consistently found across all analyses in the literature review and the Multiverse Analysis of new data. We discuss methodological parameters that may most contribute to inconsistent findings of fear extinction retention deficit in PTSD and implications for future clinical research.

Systematic comparisons of different quality control approaches applied to three large pediatric neuroimaging datasets

INTRODUCTION

Poor quality T1-weighted brain scans systematically affect the calculation of brain measures. Removing the influence of such scans requires identifying and excluding scans with noise and artefacts through a quality control (QC) procedure. While QC is critical for brain imaging analyses, it is not yet clear whether different QC approaches lead to the exclusion of the same participants. Further, the removal of poor-quality scans may unintentionally introduce a sampling bias by excluding the subset of participants who are younger and/or feature greater clinical impairment. This study had two aims: 1) examine whether different QC approaches applied to T1-weighted scans would exclude the same participants, and 2) examine how exclusion of poor-quality scans impacts specific demographic, clinical and brain measure characteristics between excluded and included participants in three large pediatric neuroimaging samples.

METHODS

We used T1-weighted, resting-state fMRI, demographic and clinical data from the Province of Ontario Neurodevelopmental Disorders network (Aim 1: n=553, Aim 2: n=465), the Healthy Brain Network (Aim 1: n=1051, Aim 2: n=558), and the Philadelphia Neurodevelopmental Cohort (Aim 1: n=1087; Aim 2: n=619). Four different QC approaches were applied to T1-weighted MRI (visual QC, metric QC, automated QC, fMRI-derived QC). We used tetrachoric correlation and inter-rater reliability analyses to examine whether different QC approaches excluded the same participants. We examined differences in age, mental health symptoms, everyday/adaptive functioning, IQ and structural MRI-derived brain indices between participants that were included versus excluded following each QC approach.

RESULTS

Dataset-specific findings revealed mixed results with respect to overlap of QC exclusion. However, in POND and HBN, we found a moderate level of overlap between visual and automated QC approaches (r_tet=0.52-0.59). Implementation of QC excluded younger participants, and tended to exclude those with lower IQ, and lower everyday/adaptive functioning scores across several approaches in a dataset-specific manner. Across nearly all datasets and QC approaches examined, excluded participants had lower estimates of cortical thickness and subcortical volume, but this effect did not differ by QC approach.

CONCLUSION

The results of this study provide insight into the influence of QC decisions on structural pediatric imaging analyses. While different QC approaches exclude different subsets of participants, the variation of influence of different QC approaches on clinical and brain metrics is minimal in large datasets. Overall, implementation of QC tends to exclude participants who are younger, and those who have more cognitive and functional impairment. Given that automated QC is standardized and can reduce between-study differences, the results of this study support the potential to use automated QC for large pediatric neuroimaging datasets.

Using preregistration as a tool for transparent fNIRS study design

Significance

The expansion of functional near-infrared spectroscopy (fNIRS) methodology and analysis tools gives rise to various design and analytical decisions that researchers have to make. Several recent efforts have developed guidelines for preprocessing, analyzing, and reporting practices. For the planning stage of fNIRS studies, similar guidance is desirable. Study preregistration helps researchers to transparently document study protocols before conducting the study, including materials, methods, and analyses, and thus, others to verify, understand, and reproduce a study. Preregistration can thus serve as a useful tool for transparent, careful, and comprehensive fNIRS study design.

Aim

We aim to create a guide on the design and analysis steps involved in fNIRS studies and to provide a preregistration template specified for fNIRS studies.

Approach

The presented preregistration guide has a strong focus on fNIRS specific requirements, and the associated template provides examples based on continuous-wave (CW) fNIRS studies conducted in humans. These can, however, be extended to other types of fNIRS studies.

Results

On a step-by-step basis, we walk the fNIRS user through key methodological and analysis-related aspects central to a comprehensive fNIRS study design. These include items specific to the design of CW, task-based fNIRS studies, but also sections that are of general importance, including an in-depth elaboration on sample size planning.

Conclusions

Our guide introduces these open science tools to the fNIRS community, providing researchers with an overview of key design aspects and specification recommendations for comprehensive study planning. As such it can be used as a template to preregister fNIRS studies or merely as a tool for transparent fNIRS study design.

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

FAIR human neuroscientific data sharing to advance AI driven research and applications: Legal frameworks and missing metadata standards

Modern AI supported research holds many promises for basic and applied science. However, the application of AI methods is often limited because most labs cannot, on their own, acquire large and diverse datasets, which are best for training these methods. Data sharing and open science initiatives promise some relief to the problem, but only if the data are provided in a usable way. The FAIR principles state very general requirements for useful data sharing: they should be findable, accessible, interoperable, and reusable. This article will focus on two challenges to implement the FAIR framework for human neuroscience data. On the one hand, human data can fall under special legal protection. The legal frameworks regulating how and what data can be openly shared differ greatly across countries which can complicate data sharing or even discourage researchers from doing so. Moreover, openly accessible data require standardization of data and metadata organization and annotation in order to become interpretable and useful. This article briefly introduces open neuroscience initiatives that support the implementation of the FAIR principles. It then reviews legal frameworks, their consequences for accessibility of human neuroscientific data and some ethical implications. We hope this comparison of legal jurisdictions helps to elucidate that some alleged obstacles for data sharing only require an adaptation of procedures but help to protect the privacy of our most generous donors to research … our study participants. Finally, it elaborates on the problem of missing standards for metadata annotation and introduces initiatives that aim at developing tools to make neuroscientific data acquisition and analysis pipelines FAIR by design. While the paper focuses on making human neuroscience data useful for data-intensive AI the general considerations hold for other fields where large amounts of openly available human data would be helpful.

Efficient evaluation of the Open QC task fMRI dataset

This article is an evaluation of the task dataset as part of the Demonstrating Quality Control (QC) Procedures in fMRI (FMRI Open QC Project) methodological research topic. The quality of both the task and fMRI aspects of the dataset are summarized in concise reports created with R, AFNI, and knitr. The reports and underlying tests are designed to highlight potential issues, are pdf files for easy archiving, and require relatively little experience to use and adapt. This article is accompanied by both the compiled reports and the source code and explanation necessary to use them.

Inter-rater reliability of functional MRI data quality control assessments: A standardised protocol and practical guide using pyfMRIqc

Quality control is a critical step in the processing and analysis of functional magnetic resonance imaging data. Its purpose is to remove problematic data that could otherwise lead to downstream errors in the analysis and reporting of results. The manual inspection of data can be a laborious and error-prone process that is susceptible to human error. The development of automated tools aims to mitigate these issues. One such tool is pyfMRIqc, which we previously developed as a user-friendly method for assessing data quality. Yet, these methods still generate output that requires subjective interpretations about whether the quality of a given dataset meets an acceptable standard for further analysis. Here we present a quality control protocol using pyfMRIqc and assess the inter-rater reliability of four independent raters using this protocol for data from the fMRI Open QC project (https://osf.io/qaesm/). Data were classified by raters as either "include," "uncertain," or "exclude." There was moderate to substantial agreement between raters for "include" and "exclude," but little to no agreement for "uncertain." In most cases only a single rater used the "uncertain" classification for a given participant's data, with the remaining raters showing agreement for "include"/"exclude" decisions in all but one case. We suggest several approaches to increase rater agreement and reduce disagreement for "uncertain" cases, aiding classification consistency.

Data management strategy for a collaborative research center

The importance of effective research data management (RDM) strategies to support the generation of Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience data grows with each advance in data acquisition techniques and research methods. To maximize the impact of diverse research strategies, multidisciplinary, large-scale neuroscience research consortia face a number of unsolved challenges in RDM. While open science principles are largely accepted, it is practically difficult for researchers to prioritize RDM over other pressing demands. The implementation of a coherent, executable RDM plan for consortia spanning animal, human, and clinical studies is becoming increasingly challenging. Here, we present an RDM strategy implemented for the Heidelberg Collaborative Research Consortium. Our consortium combines basic and clinical research in diverse populations (animals and humans) and produces highly heterogeneous and multimodal research data (e.g., neurophysiology, neuroimaging, genetics, behavior). We present a concrete strategy for initiating early-stage RDM and FAIR data generation for large-scale collaborative research consortia, with a focus on sustainable solutions that incentivize incremental RDM while respecting research-specific requirements.