Transdiagnostic psychopathology in the light of robust single-trial event-related potentials.

Recent evidence indicates that event-related potentials (ERPs) as measured on the electroencephalogram (EEG) are more closely related to transdiagnostic, dimensional measures of psychopathology (TDP) than to diagnostic categories. A comprehensive examination of correlations between well-studied ERPs and measures of TDP is called for. In this study, we recruited 50 patients with emotional disorders undergoing 14 weeks of transdiagnostic group psychotherapy as well as 37 healthy comparison subjects (HC) matched in age and sex. HCs were assessed once and patients three times throughout treatment (N = 172 data sets) with a battery of well-studied ERPs and psychopathology measures consistent with the TDP framework The Hierarchical Taxonomy of Psychopathology (HiTOP). ERPs were quantified using robust single-trial analysis (RSTA) methods and TDP correlations with linear regression models as implemented in the EEGLAB toolbox LIMO EEG. We found correlations at several levels of the HiTOP hierarchy. Among these, a reduced P3b was associated with the general p-factor. A reduced error-related negativity correlated strongly with worse symptomatology across the Internalizing spectrum. Increases in the correct-related negativity correlated with symptoms loading unto the Distress subfactor in the HiTOP. The Flanker N2 was related to specific symptoms of Intrusive Cognitions and Traumatic Re-experiencing and the mismatch negativity to maladaptive personality traits at the lowest levels of the HiTOP hierarchy. Our study highlights the advantages of RSTA methods and of using validated TDP constructs within a consistent framework. Future studies could utilize machine learning methods to predict TDP from a set of ERP features at the subject level.

Robust single-trial event-related potentials differentiate between distress and fear disorders.

Recent evidence indicates that measures of brain functioning as indexed by event-related potentials (ERPs) on the electroencephalogram align more closely to transdiagnostic measures of psychopathology than to categorical taxonomies. The Hierarchical Taxonomy of Psychopathology (HiTOP) is a transdiagnostic, dimensional framework aiming to solve issues of comorbidity, symptom heterogeneity, and arbitrary diagnostic boundaries. Based on shared features, the emotional disorders are allocated into subfactors Distress and Fear. Evidence indicates that disorders that are close in the HiTOP hierarchy share etiology, symptom profiles, and treatment outcomes. However, further studies testing the biological underpinnings of the HiTOP are called for. In this study, we assessed differences between Distress and Fear in a range of well-studied ERP components. In total, 50 patients with emotional disorders were divided into two groups (Distress, N = 25; Fear, N = 25) according to HiTOP criteria and compared against 37 healthy comparison (HC) subjects. Addressing issues in traditional ERP preprocessing and analysis methods, we applied robust single-trial analysis as implemented in the EEGLAB toolbox LIMO EEG. Several ERP components were found to differ between the groups. Surprisingly, we found no difference between Fear and HC for any of the ERPs. This suggests that some well-established results from the literature, e.g., increased error-related negativity in OCD, are not a shared neurobiological correlate of the Fear subfactor. Conversely, for Distress, we found reductions compared to Fear and HC in several ERP components across paradigms. Future studies could utilize HiTOP-validated psychopathology measures to more precisely define subfactor groups.

On the Long-term Archiving of Research Data.

Accessing research data at any time is what FAIR (Findable Accessible Interoperable Reusable) data sharing aims to achieve at scale. Yet, we argue that it is not sustainable to keep accumulating and maintaining all datasets for rapid access, considering the monetary and ecological cost of maintaining repositories. Here, we address the issue of cold data storage: when to dispose of data for offline storage, how can this be done while maintaining FAIR principles and who should be responsible for cold archiving and long-term preservation.

Biases in BCI experiments: Do we really need to balance stimulus properties across categories?

Brain Computer Interfaces (BCIs) consist of an interaction between humans and computers with a specific mean of communication, such as voice, gestures, or even brain signals that are usually recorded by an Electroencephalogram (EEG). To ensure an optimal interaction, the BCI algorithm typically involves the classification of the input signals into predefined task-specific categories. However, a recurrent problem is that the classifier can easily be biased by uncontrolled experimental conditions, namely covariates, that are unbalanced across the categories. This issue led to the current solution of forcing the balance of these covariates across the different categories which is time consuming and drastically decreases the dataset diversity. The purpose of this research is to evaluate the need for this forced balance in BCI experiments involving EEG data. A typical design of neural BCIs involves repeated experimental trials using visual stimuli to trigger the so-called Event-Related Potential (ERP). The classifier is expected to learn spatio-temporal patterns specific to categories rather than patterns related to uncontrolled stimulus properties, such as psycho-linguistic variables (e.g., phoneme number, familiarity, and age of acquisition) and image properties (e.g., contrast, compactness, and homogeneity). The challenges are then to know how biased the decision is, which features affect the classification the most, which part of the signal is impacted, and what is the probability to perform neural categorization per se. To address these problems, this research has two main objectives: (1) modeling and quantifying the covariate effects to identify spatio-temporal regions of the EEG allowing maximal classification performance while minimizing the biasing effect, and (2) evaluating the need to balance the covariates across categories when studying brain mechanisms. To solve the modeling problem, we propose using a linear parametric analysis applied to some observable and commonly studied covariates to them. The biasing effect is quantified by comparing the regions highly influenced by the covariates with the regions of high categorical contrast, i.e., parts of the ERP allowing a reliable classification. The need to balance the stimulus's inner properties across categories is evaluated by assessing the separability between category-related and covariate-related evoked responses. The procedure is applied to a visual priming experiment where the images represent items belonging to living or non-living entities. The observed covariates are the commonly controlled psycho-linguistic variables and some visual features of the images. As a result, we identified that the category of the stimulus mostly affects the late evoked response. The covariates, when not modeled, have a biasing effect on the classification, essentially in the early evoked response. This effect increases with the diversity of the dataset and the complexity of the algorithm used. As the effects of both psycho-linguistic variables and image features appear outside of the spatio-temporal regions of significant categorical contrast, the proper selection of the region of interest makes the classification reliable. Having proved that the covariate effects can be separated from the categorical effect, our framework can be further used to isolate the category-dependent evoked response from the rest of the EEG to study neural processes involved when seeing living vs. non-living entities.

Open and reproducible neuroimaging: From study inception to publication.

Empirical observations of how labs conduct research indicate that the adoption rate of open practices for transparent, reproducible, and collaborative science remains in its infancy. This is at odds with the overwhelming evidence for the necessity of these practices and their benefits for individual researchers, scientific progress, and society in general. To date, information required for implementing open science practices throughout the different steps of a research project is scattered among many different sources. Even experienced researchers in the topic find it hard to navigate the ecosystem of tools and to make sustainable choices. Here, we provide an integrated overview of community-developed resources that can support collaborative, open, reproducible, replicable, robust and generalizable neuroimaging throughout the entire research cycle from inception to publication and across different neuroimaging modalities. We review tools and practices supporting study inception and planning, data acquisition, research data management, data processing and analysis, and research dissemination. An online version of this resource can be found at https://oreoni.github.io. We believe it will prove helpful for researchers and institutions to make a successful and sustainable move towards open and reproducible science and to eventually take an active role in its future development.

The Open-Access European Prevention of Alzheimer's Dementia (EPAD) MRI dataset and processing workflow.

The European Prevention of Alzheimer Dementia (EPAD) is a multi-center study that aims to characterize the preclinical and prodromal stages of Alzheimer's Disease. The EPAD imaging dataset includes core (3D T1w, 3D FLAIR) and advanced (ASL, diffusion MRI, and resting-state fMRI) MRI sequences. Here, we give an overview of the semi-automatic multimodal and multisite pipeline that we developed to curate, preprocess, quality control (QC), and compute image-derived phenotypes (IDPs) from the EPAD MRI dataset. This pipeline harmonizes DICOM data structure across sites and performs standardized MRI preprocessing steps. A semi-automated MRI QC procedure was implemented to visualize and flag MRI images next to site-specific distributions of QC features - i.e. metrics that represent image quality. The value of each of these QC features was evaluated through comparison with visual assessment and step-wise parameter selection based on logistic regression. IDPs were computed from 5 different MRI modalities and their sanity and potential clinical relevance were ascertained by assessing their relationship with biological markers of aging and dementia. The EPAD v1500.0 data release encompassed core structural scans from 1356 participants 842 fMRI, 831 dMRI, and 858 ASL scans. From 1356 3D T1w images, we identified 17 images with poor quality and 61 with moderate quality. Five QC features - Signal to Noise Ratio (SNR), Contrast to Noise Ratio (CNR), Coefficient of Joint Variation (CJV), Foreground-Background energy Ratio (FBER), and Image Quality Rate (IQR) - were selected as the most informative on image quality by comparison with visual assessment. The multimodal IDPs showed greater impairment in associations with age and dementia biomarkers, demonstrating the potential of the dataset for future clinical analyses.

Coupling cognitive and brainstem dysfunction in multiple sclerosis-related chronic neuropathic limb pain.

Chronic pain in multiple sclerosis is common and difficult to treat. Its mechanisms remain incompletely understood. Dysfunction of the descending pain modulatory system is known to contribute to human chronic pain conditions. However, it is not clear how alterations in executive function influence this network, despite healthy volunteer studies linking function of the descending pain modulatory system, to cognition. In adults with multiple sclerosis-associated chronic neuropathic limb pain, compared to those without pain, we hypothesized altered functional connectivity of the descending pain modulatory system, coupled to executive dysfunction. Specifically we hypothesized reduced mental flexibility, because of potential importance in stimulus reappraisal. To investigate these hypotheses, we conducted a case-control cross-sectional study of 47 adults with relapsing remitting multiple sclerosis (31 with chronic neuropathic limb pain, 16 without pain), employing clinical, neuropsychological, structural, and functional MRI measures. We measured brain lesions and atrophy affecting descending pain modulatory system structures. Both cognitive and affective dysfunctions were confirmed in the chronic neuropathic limb pain group, including reduced mental flexibility (Delis Kaplan Executive Function System card sorting tests P < 0.001). Functional connectivity of rostral anterior cingulate and ventrolateral periaqueductal gray, key structures of the descending pain modulatory system, was significantly lower in the group experiencing chronic neuropathic pain. There was no significant between-group difference in whole-brain grey matter or lesion volumes, nor lesion volume affecting white matter tracts between rostral anterior cingulate and periaqueductal gray. Brainstem-specific lesion volume was higher in the chronic neuropathic limb pain group (P = 0.0017). Differential functional connectivity remained after correction for brainstem-specific lesion volume. Gabapentinoid medications were more frequently used in the chronic pain group. We describe executive dysfunction in people with multiple sclerosis affected by chronic neuropathic pain, along with functional and structural MRI evidence compatible with dysfunction of the descending pain modulatory system. These findings extend understanding of close inter-relationships between cognition, function of the descending pain modulatory system, and chronic pain, both in multiple sclerosis and more generally in human chronic pain conditions. These findings could support application of pharmacological and cognitive interventions in chronic neuropathic pain associated with multiple sclerosis.

A systematic review on the use of quantitative imaging to detect cancer therapy adverse effects in normal-appearing brain tissue.

Cancer therapy for both central nervous system (CNS) and non-CNS tumors has been previously associated with transient and long-term cognitive deterioration, commonly referred to as 'chemo fog'. This therapy-related damage to otherwise normal-appearing brain tissue is reported using post-mortem neuropathological analysis. Although the literature on monitoring therapy effects on structural magnetic resonance imaging (MRI) is well established, such macroscopic structural changes appear relatively late and irreversible. Early quantitative MRI biomarkers of therapy-induced damage would potentially permit taking these treatment side effects into account, paving the way towards a more personalized treatment planning.This systematic review (PROSPERO number 224196) provides an overview of quantitative tomographic imaging methods, potentially identifying the adverse side effects of cancer therapy in normal-appearing brain tissue. Seventy studies were obtained from the MEDLINE and Web of Science databases. Studies reporting changes in normal-appearing brain tissue using MRI, PET, or SPECT quantitative biomarkers, related to radio-, chemo-, immuno-, or hormone therapy for any kind of solid, cystic, or liquid tumor were included. The main findings of the reviewed studies were summarized, providing also the risk of bias of each study assessed using a modified QUADAS-2 tool. For each imaging method, this review provides the methodological background, and the benefits and shortcomings of each method from the imaging perspective. Finally, a set of recommendations is proposed to support future research.

#EEGManyLabs: Investigating the replicability of influential EEG experiments.

There is growing awareness across the neuroscience community that the replicability of findings about the relationship between brain activity and cognitive phenomena can be improved by conducting studies with high statistical power that adhere to well-defined and standardised analysis pipelines. Inspired by recent efforts from the psychological sciences, and with the desire to examine some of the foundational findings using electroencephalography (EEG), we have launched #EEGManyLabs, a large-scale international collaborative replication effort. Since its discovery in the early 20th century, EEG has had a profound influence on our understanding of human cognition, but there is limited evidence on the replicability of some of the most highly cited discoveries. After a systematic search and selection process, we have identified 27 of the most influential and continually cited studies in the field. We plan to directly test the replicability of key findings from 20 of these studies in teams of at least three independent laboratories. The design and protocol of each replication effort will be submitted as a Registered Report and peer-reviewed prior to data collection. Prediction markets, open to all EEG researchers, will be used as a forecasting tool to examine which findings the community expects to replicate. This project will update our confidence in some of the most influential EEG findings and generate a large open access database that can be used to inform future research practices. Finally, through this international effort, we hope to create a cultural shift towards inclusive, high-powered multi-laboratory collaborations.

Transcranial ultrasound pulse stimulation reduces cortical atrophy in Alzheimer's patients: A follow-up study.

INTRODUCTION: Ultrasound for the brain is a revolutionary therapeutic concept. The first clinical data indicate that 2-4 weeks of therapy with transcranial pulse stimulation (TPS) improve functional networks and cognitive performance of Alzheimer's disease (AD) patients for up to 3 months. No data currently exist on possible benefits concerning brain morphology, namely the cortical atrophy characteristic of AD. METHODS: We performed a pre-/post-therapy analysis of cortical thickness in a group of N = 17 AD patients. RESULTS: We found a significant correlation between neuropsychological improvement and cortical thickness increase in AD-critical brain areas. DISCUSSION: AD patients who benefit from TPS appear to manifest reduced cortical atrophy within the default mode network in particular, whose memory-related subsystems are believed to be disrupted in AD. TPS may therefore hold promise as a new add-on therapy for AD.

Mindfulness related changes in grey matter: a systematic review and meta-analysis.

Knowing target regions undergoing strfuncti changes caused by behavioural interventions is paramount in evaluating the effectiveness of such practices. Here, using a systematic review approach, we identified 25 peer-reviewed magnetic resonance imaging (MRI) studies demonstrating grey matter changes related to mindfulness meditation. An activation likelihood estimation (ALE) analysis (n = 16) revealed the right anterior ventral insula as the only significant region with consistent effect across studies, whilst an additional functional connectivity analysis indicates that both left and right insulae, and the anterior cingulate gyrus with adjacent paracingulate gyri should also be considered in future studies. Statistical meta-analyses suggest medium to strong effect sizes from Cohen's d ~ 0.8 in the right insula to ~ 1 using maxima across the whole brain. The systematic review revealed design issues with selection, information, attrition and confirmation biases, in addition to weak statistical power. In conclusion, our analyses show that mindfulness meditation practice does induce grey matter changes but also that improvements in methodology are needed to establish mindfulness as a therapeutic intervention.

The Open Brain Consent: Informing research participants and obtaining consent to share brain imaging data.

Having the means to share research data openly is essential to modern science. For human research, a key aspect in this endeavor is obtaining consent from participants, not just to take part in a study, which is a basic ethical principle, but also to share their data with the scientific community. To ensure that the participants' privacy is respected, national and/or supranational regulations and laws are in place. It is, however, not always clear to researchers what the implications of those are, nor how to comply with them. The Open Brain Consent (https://open-brain-consent.readthedocs.io) is an international initiative that aims to provide researchers in the brain imaging community with information about data sharing options and tools. We present here a short history of this project and its latest developments, and share pointers to consent forms, including a template consent form that is compliant with the EU general data protection regulation. We also share pointers to an associated data user agreement that is not only useful in the EU context, but also for any researchers dealing with personal (clinical) data elsewhere.

GliMR: Cross-Border Collaborations to Promote Advanced MRI Biomarkers for Glioma.

Purpose: There is an annual incidence of 50,000 glioma cases in Europe. The optimal treatment strategy is highly personalised, depending on tumour type, grade, spatial localization, and the degree of tissue infiltration. In research settings, advanced magnetic resonance imaging (MRI) has shown great promise as a tool to inform personalised treatment decisions. However, the use of advanced MRI in clinical practice remains scarce due to the downstream effects of siloed glioma imaging research with limited representation of MRI specialists in established consortia; and the associated lack of available tools and expertise in clinical settings. These shortcomings delay the translation of scientific breakthroughs into novel treatment strategy. As a response we have developed the network "Glioma MR Imaging 2.0" (GliMR) which we present in this article. Methods: GliMR aims to build a pan-European and multidisciplinary network of experts and accelerate the use of advanced MRI in glioma beyond the current "state-of-the-art" in glioma imaging. The Action Glioma MR Imaging 2.0 (GliMR) was granted funding by the European Cooperation in Science and Technology (COST) in June 2019. Results: GliMR's first grant period ran from September 2019 to April 2020, during which several meetings were held and projects were initiated, such as reviewing the current knowledge on advanced MRI; developing a General Data Protection Regulation (GDPR) compliant consent form; and setting up the website. Conclusion: The Action overcomes the pre-existing limitations of glioma research and is funded until September 2023. New members will be accepted during its entire duration.

The genetics-BIDS extension: Easing the search for genetic data associated with human brain imaging.

Metadata are what makes databases searchable. Without them, researchers would have difficulty finding data with features they are interested in. Brain imaging genetics is at the intersection of two disciplines, each with dedicated dictionaries and ontologies facilitating data search and analysis. Here, we present the genetics Brain Imaging Data Structure extension, consisting of metadata files for human brain imaging data to which they are linked, and describe succinctly the genomic and transcriptomic data associated with them, which may be in different databases. This extension will facilitate identifying micro-scale molecular features that are linked to macro-scale imaging repositories, facilitating data aggregation across studies.

Issues and recommendations from the OHBM COBIDAS MEEG committee for reproducible EEG and MEG research.

The Organization for Human Brain Mapping (OHBM) has been active in advocating for the instantiation of best practices in neuroimaging data acquisition, analysis, reporting and sharing of both data and analysis code to deal with issues in science related to reproducibility and replicability. Here we summarize recommendations for such practices in magnetoencephalographic (MEG) and electroencephalographic (EEG) research, recently developed by the OHBM neuroimaging community known by the abbreviated name of COBIDAS MEEG. We discuss the rationale for the guidelines and their general content, which encompass many topics under active discussion in the field. We highlight future opportunities and challenges to maximizing the sharing and exploitation of MEG and EEG data, and we also discuss how this 'living' set of guidelines will evolve to continually address new developments in neurophysiological assessment methods and multimodal integration of neurophysiological data with other data types.

From BIDS-Formatted EEG Data to Sensor-Space Group Results: A Fully Reproducible Workflow With EEGLAB and LIMO EEG.

Reproducibility is a cornerstone of scientific communication without which one cannot build upon each other's work. Because modern human brain imaging relies on many integrated steps with a variety of possible algorithms, it has, however, become impossible to report every detail of a data processing workflow. In response to this analytical complexity, community recommendations are to share data analysis pipelines (scripts that implement workflows). Here we show that this can easily be done using EEGLAB and tools built around it. BIDS tools allow importing all the necessary information and create a study from electroencephalography (EEG)-Brain Imaging Data Structure compliant data. From there preprocessing can be carried out in only a few steps using EEGLAB and statistical analyses performed using the LIMO EEG plug-in. Using Wakeman and Henson (2015) face dataset, we illustrate how to prepare data and build different statistical models, a standard factorial design (faces ∗ repetition), and a more modern trial-based regression approach for the stimulus repetition effect, all in a few reproducible command lines.

The use of brain functional magnetic resonance imaging to determine the mechanism of action of gabapentin in managing chronic pelvic pain in women: a pilot study.

OBJECTIVE: To inform feasibility and design of a future randomised controlled trial (RCT) using brain functional MRI (fMRI) to determine the mechanism of action of gabapentin in managing chronic pelvic pain (CPP) in women. DESIGN: Mechanistic study embedded in pilot RCT. SETTING: University Hospital. PARTICIPANTS: Twelve women (18-50 years) with CPP and no pelvic pathology (follow-up completed March 2014). INTERVENTION: Oral gabapentin (300-2700 mg) or matched placebo. OUTCOME MEASURES: After 12 weeks of treatment, participants underwent fMRI of the brain (Verio Siemens 3T MRI) during which noxious heat and punctate stimuli were delivered to the pelvis and arm. Outcome measures included pain (visual analogue scale), blood oxygen level dependent signal change and a semi-structured acceptability questionnaire at study completion prior to unblinding. RESULTS: Full datasets were obtained for 11 participants. Following noxious heat to the abdomen, the gabapentin group (GG) had lower pain scores (Mean: 3.8 [SD 2.2]) than the placebo group (PG) (Mean: 5.8 [SD 0.9]). This was also the case for noxious heat to the arm with the GG having lower pain scores (Mean: 2.6 [SD 2.5]) than the PG (Mean: 6.2 [SD 1.1]). Seven out of 12 participants completed the acceptability questionnaire. 71% (five out of seven) described their participation in the fMRI study as positive; the remaining two rated it as a negative experience. CONCLUSIONS: Incorporating brain fMRI in a future RCT to determine the mechanism of action of gabapentin in managing CPP in women was feasible and acceptable to most women. TRIAL REGISTRATION NUMBER: ISRCTN70960777.