Sharing individualised template MRI data for MEG source reconstruction: A solution for open data while keeping subject confidentiality

Magnetoencephalography Atlas Viewer for Dipole Localization and Viewing

Magnetoencephalography (MEG) is a noninvasive neuroimaging technique widely recognized for epilepsy and tumor mapping. MEG clinical reporting requires a multidisciplinary team, including expert input regarding each dipole's anatomic localization. Here, we introduce a novel tool, the "Magnetoencephalography Atlas Viewer" (MAV), which streamlines this anatomical analysis. The MAV normalizes the patient's Magnetic Resonance Imaging (MRI) to the Montreal Neurological Institute (MNI) space, reverse-normalizes MNI atlases to the native MRI, identifies MEG dipole files, and matches dipoles' coordinates to their spatial location in atlas files. It offers a user-friendly and interactive graphical user interface (GUI) for displaying individual dipoles, groups, coordinates, anatomical labels, and a tri-planar MRI view of the patient with dipole overlays. It evaluated over 273 dipoles obtained in clinical epilepsy subjects. Consensus-based ground truth was established by three neuroradiologists, with a minimum agreement threshold of two. The concordance between the ground truth and MAV labeling ranged from 79% to 84%, depending on the normalization method. Higher concordance rates were observed in subjects with minimal or no structural abnormalities on the MRI, ranging from 80% to 90%. The MAV provides a straightforward MEG dipole anatomic localization method, allowing a nonspecialist to prepopulate a report, thereby facilitating and reducing the time of clinical reporting.

Oscillatory and non-oscillatory features of the magnetoencephalic sensorimotor rhythm in Parkinson's disease

Parkinson's disease (PD) is associated with changes in neural activity in the sensorimotor alpha and beta bands. Using magnetoencephalography (MEG), we investigated the role of spontaneous neuronal activity within the somatosensory cortex in a large cohort of early- to mid-stage PD patients (N = 78) on Parkinsonian medication and age- and sex-matched healthy controls (N = 60) using source reconstructed resting-state MEG. We quantified features of the time series data in terms of oscillatory alpha power and central alpha frequency, beta power and central beta frequency, and 1/f broadband characteristics using power spectral density. Furthermore, we characterised transient oscillatory burst events in the mu-beta band time-domain signals. We examined the relationship between these signal features and the patients' disease state, symptom severity, age, sex, and cortical thickness. PD patients and healthy controls differed on PSD broadband characteristics, with PD patients showing a steeper 1/f exponential slope and higher 1/f offset. PD patients further showed a steeper age-related decrease in the burst rate. Out of all the signal features of the sensorimotor activity, the burst rate was associated with increased severity of bradykinesia, whereas the burst duration was associated with axial symptoms. Our study shows that general non-oscillatory features (broadband 1/f exponent and offset) of the sensorimotor signals are related to disease state and oscillatory burst rate scales with symptom severity in PD.

The Swedish National Facility for Magnetoencephalography Parkinson's disease dataset

Parkinson's disease (PD) is characterised by a loss of dopamine and dopaminergic cells. The consequences hereof are widespread network disturbances in brain function. It is an ongoing topic of investigation how the disease-related changes in brain function manifest in PD relate to clinical symptoms. We present The Swedish National Facility for Magnetoencephalography Parkinson's Disease Dataset (NatMEG-PD) as an Open Science contribution to identify the functional neural signatures of Parkinson's disease and contribute to diagnosis and treatment. The dataset contains whole-head magnetoencephalographic (MEG) recordings from 66 well-characterised PD patients on their regular dose of dopamine replacement therapy and 68 age- and sex-matched healthy controls. NatMEG-PD contains three-minute eyes-closed resting-state MEG, MEG during an active movement task, and MEG during passive movements. The data includes anonymised MRI for source analysis and clinical scores. MEG data is rich in nature and can be used to explore numerous functional features. By sharing these data, we hope other researchers will contribute to advancing our understanding of the relationship between brain activity and disease state or symptoms.

Ethics Along the Continuum of Research Involving Persons with Disorders of Consciousness

Interest in disorders of consciousness (DoC) has grown substantially over the past decade and has illuminated the importance of improving understanding of DoC biology; care needs (use of monitoring, performance of interventions, and provision of emotional support); treatment options to promote recovery; and outcome prediction. Exploration of these topics requires awareness of numerous ethics considerations related to rights and resources. The Curing Coma Campaign Ethics Working Group used its expertise in neurocritical care, neuropalliative care, neuroethics, neuroscience, philosophy, and research to formulate an informal review of ethics considerations along the continuum of research involving persons with DoC related to the following: (1) study design; (2) comparison of risks versus benefits; (3) selection of inclusion and exclusion criteria; (4) screening, recruitment, and enrollment; (5) consent; (6) data protection; (7) disclosure of results to surrogates and/or legally authorized representatives; (8) translation of research into practice; (9) identification and management of conflicts of interest; (10) equity and resource availability; and (11) inclusion of minors with DoC in research. Awareness of these ethics considerations when planning and performing research involving persons with DoC will ensure that the participant rights are respected while maximizing the impact and meaningfulness of the research, interpretation of outcomes, and communication of results.

Deep learning based source imaging provides strong sublobar localization of epileptogenic zone from MEG interictal spikes

Electromagnetic source imaging (ESI) offers unique capability of imaging brain dynamics for studying brain functions and aiding the clinical management of brain disorders. Challenges exist in ESI due to the ill-posedness of the inverse problem and thus the need of modeling the underlying brain dynamics for regularizations. Advances in generative models provide opportunities for more accurate and realistic source modeling that could offer an alternative approach to ESI for modeling the underlying brain dynamics beyond equivalent physical source models. However, it is not straightforward to explicitly formulate the knowledge arising from these generative models within the conventional ESI framework. Here we investigate a novel source imaging framework based on mesoscale neuronal modeling and deep learning (DL) that can learn the sensor-source mapping relationship directly from MEG data for ESI. Two DL-based ESI models were trained based on data generated by neural mass models and either generic or personalized head models. The robustness of the two DL models was evaluated by systematic computer simulations and clinical validation in a cohort of 29 drug-resistant focal epilepsy patients who underwent intracranial EEG (iEEG) evaluation or surgical resection. Results estimated from pre-operative MEG interictal spikes were quantified using the overlap with resection regions and the distance to the seizure-onset zone (SOZ) defined by iEEG recordings. The DL-based ESI provided robust results when no personalized head geometry is considered, reaching a spatial dispersion of 21.90 ± 19.03 mm, sublobar concordance of 83 %, and sublobar sensitivity and specificity of 66 and 97 % respectively. When using personalized head geometry derived from individual patients' MRI in the training data, personalized DL-based ESI model can further improve the performance and reached a spatial dispersion of 8.19 ± 8.14 mm, sublobar concordance of 93 %, and sublobar sensitivity and specificity of 77 and 99 % respectively. When compared to the SOZ, the localization error of the personalized approach is 15.78 ± 5.54 mm, outperforming the conventional benchmarks. This work demonstrates that combining generative models and deep learning enables an accurate and robust imaging of epileptogenic zone from MEG recordings with strong sublobar precision, suggesting its added value to enhancing MEG source localization and imaging, and to epilepsy source localization and other clinical applications.

MEG frequency tagging reveals a grid-like code during attentional movements

Grid-cells firing fields tile the environment with a 6-fold periodicity during both locomotion and visual exploration. Here, we tested, in humans, whether movements of covert attention elicit grid-like coding using frequency tagging. Participants observed visual trajectories presented sequentially at fixed rate, allowing different spatial periodicities (e.g., 4-, 6-, and 8-fold) to have corresponding temporal periodicities (e.g., 1, 1.5, and 2 Hz), thus resulting in distinct spectral responses. We found a higher response for the (grid-like) 6-fold periodicity and localized this effect in medial-temporal sources. In a control experiment featuring the same temporal periodicity but lacking spatial structure, the 6-fold effect did not emerge, suggesting its dependency on spatial movements of attention. We report evidence that grid-like signals in the human medial-temporal lobe can be elicited by covert attentional movements and suggest that attentional coding may provide a suitable mechanism to support the activation of cognitive maps during conceptual navigation.

Modular pipeline for reconstruction and localization of implanted intracranial ECoG and sEEG electrodes

Implantation of electrodes in the brain has been used as a clinical tool for decades to stimulate and record brain activity. As this method increasingly becomes the standard of care for several disorders and diseases, there is a growing need to quickly and accurately localize the electrodes once they are placed within the brain. We share here a protocol pipeline for localizing electrodes implanted in the brain, which we have applied to more than 260 patients, that is accessible to multiple skill levels and modular in execution. This pipeline uses multiple software packages to prioritize flexibility by permitting multiple different parallel outputs while minimizing the number of steps for each output. These outputs include co-registered imaging, electrode coordinates, 2D and 3D visualizations of the implants, automatic surface and volumetric localizations of the brain regions per electrode, and anonymization and data sharing tools. We demonstrate here some of the pipeline's visualizations and automatic localization algorithms which we have applied to determine appropriate stimulation targets, to conduct seizure dynamics analysis, and to localize neural activity from cognitive tasks in previous studies. Further, the output facilitates the extraction of information such as the probability of grey matter intersection or the nearest anatomic structure per electrode contact across all data sets that go through the pipeline. We expect that this pipeline will be a useful framework for researchers and clinicians alike to localize implanted electrodes in the human brain.

Modified MRI Anonymization (De-Facing) for Improved MEG Coregistration

Localising the sources of MEG/EEG signals often requires a structural MRI to create a head model, while ensuring reproducible scientific results requires sharing data and code. However, sharing structural MRI data often requires the face go be hidden to help protect the identity of the individuals concerned. While automated de-facing methods exist, they tend to remove the whole face, which can impair methods for coregistering the MRI data with the EEG/MEG data. We show that a new, automated de-facing method that retains the nose maintains good MRI-MEG/EEG coregistration. Importantly, behavioural data show that this "face-trimming" method does not increase levels of identification relative to a standard de-facing approach and has less effect on the automated segmentation and surface extraction sometimes used to create head models for MEG/EEG localisation. We suggest that this trimming approach could be employed for future sharing of structural MRI data, at least for those to be used in forward modelling (source reconstruction) of EEG/MEG data.

Advances in human intracranial electroencephalography research, guidelines and good practices

Since the second-half of the twentieth century, intracranial electroencephalography (iEEG), including both electrocorticography (ECoG) and stereo-electroencephalography (sEEG), has provided an intimate view into the human brain. At the interface between fundamental research and the clinic, iEEG provides both high temporal resolution and high spatial specificity but comes with constraints, such as the individual's tailored sparsity of electrode sampling. Over the years, researchers in neuroscience developed their practices to make the most of the iEEG approach. Here we offer a critical review of iEEG research practices in a didactic framework for newcomers, as well addressing issues encountered by proficient researchers. The scope is threefold: (i) review common practices in iEEG research, (ii) suggest potential guidelines for working with iEEG data and answer frequently asked questions based on the most widespread practices, and (iii) based on current neurophysiological knowledge and methodologies, pave the way to good practice standards in iEEG research. The organization of this paper follows the steps of iEEG data processing. The first section contextualizes iEEG data collection. The second section focuses on localization of intracranial electrodes. The third section highlights the main pre-processing steps. The fourth section presents iEEG signal analysis methods. The fifth section discusses statistical approaches. The sixth section draws some unique perspectives on iEEG research. Finally, to ensure a consistent nomenclature throughout the manuscript and to align with other guidelines, e.g., Brain Imaging Data Structure (BIDS) and the OHBM Committee on Best Practices in Data Analysis and Sharing (COBIDAS), we provide a glossary to disambiguate terms related to iEEG research.