Real-time fMRI data for testing OpenNFT functionality

The Journey of the Default Mode Network: Development, Function, and Impact on Mental Health

The Default Mode Network has been extensively studied in recent decades due to its central role in higher cognitive processes and its relevance for understanding mental disorders. This neural network, characterized by synchronized and coherent activity at rest, is intrinsically linked to self-reflection, mental exploration, social interaction, and emotional processing. Our understanding of the DMN extends beyond humans to non-human animals, where it has been observed in various species, highlighting its evolutionary basis and adaptive significance throughout phylogenetic history. Additionally, the DMN plays a crucial role in brain development during childhood and adolescence, influencing fundamental cognitive and emotional processes. This literature review aims to provide a comprehensive overview of the DMN, addressing its structural, functional, and evolutionary aspects, as well as its impact from infancy to adulthood. By gaining a deeper understanding of the organization and function of the DMN, we can advance our knowledge of the neural mechanisms that underlie cognition, behavior, and mental health. This, in turn, can lead to more effective therapeutic strategies for a range of neuropsychiatric conditions.

Exploring protocol development: Implementing systematic contextual memory to enhance real-time fMRI neurofeedback

Objective

The goal of this study was to explore the development and implementation of a protocol for real-time fMRI neurofeedback (rtfMRI-nf) and to assess the potential for enhancing the selective brain activation using stimuli from Virtual Reality (VR). In this study we focused on two specific brain regions, supplementary motor area (SMA) and right inferior frontal gyrus (rIFG). Publications by other study groups have suggested impaired function in these specific brain regions in patients with the diagnoses Attention Deficit Hyperactivity Disorder (ADHD) and Tourette's Syndrome (TS). This study explored the development of a protocol to investigate if attention and contextual memory may be used to systematically strengthen the procedure of rtfMRI-nf.

Methods

We used open-science software and platforms for rtfMRI-nf and for developing a simulated repetition of the rtfMRI-nf brain training in VR. We conducted seven exploratory tests in which we updated the protocol at each step. During rtfMRI-nf, MRI images are analyzed live while a person is undergoing an MRI scan, and the results are simultaneously shown to the person in the MRI-scanner. By focusing the analysis on specific regions of the brain, this procedure can be used to help the person strengthen conscious control of these regions. The VR simulation of the same experience involved a walk through the hospital toward the MRI scanner where the training sessions were conducted, as well as a subsequent simulated repetition of the MRI training. The VR simulation was a 2D projection of the experience.The seven exploratory tests involved 19 volunteers. Through this exploration, methods for aiming within the brain (e.g. masks/algorithms for coordinate-system control) and calculations for the analyses (e.g. calculations based on connectivity versus activity) were updated by the project team throughout the project. The final procedure involved three initial rounds of rtfMRI-nf for learning brain strategies. Then, the volunteers were provided with VR headsets and given instructions for one week of use. Afterward, a new session with three rounds of rtfMRI-nf was conducted.

Results

Through our exploration of the indirect effect parameters - brain region activity (directed oxygenated blood flow), connectivity (degree of correlated activity in different regions), and neurofeedback score - the volunteers tended to increase activity in the reinforced brain regions through our seven tests. Updates of procedures and analyses were always conducted between pilots, and never within. The VR simulated repetition was tested in pilot 7, but the role of the VR contribution in this setting is unclear due to underpowered testing.

Conclusion

This proof-of-concept protocol implies how rtfMRI-nf may be used to selectively train two brain regions (SMA and rIFG). The method may likely be adapted to train any given region in the brain, but readers are advised to update and adapt the procedure to experimental needs.

Real-time and Recursive Estimators for Functional MRI Quality Assessment

Real-time quality assessment (rtQA) of functional magnetic resonance imaging (fMRI) based on blood oxygen level-dependent (BOLD) signal changes is critical for neuroimaging research and clinical applications. The losses of BOLD sensitivity because of different types of technical and physiological noise remain major sources of fMRI artifacts. Due to difficulty of subjective visual perception of image distortions during data acquisitions, a comprehensive automatic rtQA is needed. To facilitate rapid rtQA of fMRI data, we applied real-time and recursive quality assessment methods to whole-brain fMRI volumes, as well as time-series of target brain areas and resting-state networks. We estimated recursive temporal signal-to-noise ratio (rtSNR) and contrast-to-noise ratio (rtCNR), and real-time head motion parameters by a framewise rigid-body transformation (translations and rotations) using the conventional current to template volume registration. In addition, we derived real-time framewise (FD) and micro (MD) displacements based on head motion parameters and evaluated the temporal derivative of root mean squared variance over voxels (DVARS). For monitoring time-series of target regions and networks, we estimated the number of spikes and amount of filtered noise by means of a modified Kalman filter. Finally, we applied the incremental general linear modeling (GLM) to evaluate real-time contributions of nuisance regressors (linear trend and head motion). Proposed rtQA was demonstrated in real-time fMRI neurofeedback runs without and with excessive head motion and real-time simulations of neurofeedback and resting-state fMRI data. The rtQA was implemented as an extension of the open-source OpenNFT software written in Python, MATLAB and C++ for neurofeedback, task-based, and resting-state paradigms. We also developed a general Python library to unify real-time fMRI data processing and neurofeedback applications. Flexible estimation and visualization of rtQA facilitates efficient rtQA of fMRI data and helps the robustness of fMRI acquisitions by means of substantiating decisions about the necessity of the interruption and re-start of the experiment and increasing the confidence in neural estimates.

BrainIAK: The Brain Imaging Analysis Kit

Functional magnetic resonance imaging (fMRI) offers a rich source of data for studying the neural basis of cognition. Here, we describe the Brain Imaging Analysis Kit (BrainIAK), an open-source, free Python package that provides computationally optimized solutions to key problems in advanced fMRI analysis. A variety of techniques are presently included in BrainIAK: intersubject correlation (ISC) and intersubject functional connectivity (ISFC), functional alignment via the shared response model (SRM), full correlation matrix analysis (FCMA), a Bayesian version of representational similarity analysis (BRSA), event segmentation using hidden Markov models, topographic factor analysis (TFA), inverted encoding models (IEMs), an fMRI data simulator that uses noise characteristics from real data (fmrisim), and some emerging methods. These techniques have been optimized to leverage the efficiencies of high-performance compute (HPC) clusters, and the same code can be se amlessly transferred from a laptop to a cluster. For each of the aforementioned techniques, we describe the data analysis problem that the technique is meant to solve and how it solves that problem; we also include an example Jupyter notebook for each technique and an annotated bibliography of papers that have used and/or described that technique. In addition to the sections describing various analysis techniques in BrainIAK, we have included sections describing the future applications of BrainIAK to real-time fMRI, tutorials that we have developed and shared online to facilitate learning the techniques in BrainIAK, computational innovations in BrainIAK, and how to contribute to BrainIAK. We hope that this manuscript helps readers to understand how BrainIAK might be useful in their research.

Quality and denoising in real-time functional magnetic resonance imaging neurofeedback: A methods review

Neurofeedback training using real-time functional magnetic resonance imaging (rtfMRI-NF) allows subjects voluntary control of localised and distributed brain activity. It has sparked increased interest as a promising non-invasive treatment option in neuropsychiatric and neurocognitive disorders, although its efficacy and clinical significance are yet to be determined. In this work, we present the first extensive review of acquisition, processing and quality control methods available to improve the quality of the neurofeedback signal. Furthermore, we investigate the state of denoising and quality control practices in 128 recently published rtfMRI-NF studies. We found: (a) that less than a third of the studies reported implementing standard real-time fMRI denoising steps, (b) significant room for improvement with regards to methods reporting and (c) the need for methodological studies quantifying and comparing the contribution of denoising steps to the neurofeedback signal quality. Advances in rtfMRI-NF research depend on reproducibility of methods and results. Notably, a systematic effort is needed to build up evidence that disentangles the various mechanisms influencing neurofeedback effects. To this end, we recommend that future rtfMRI-NF studies: (a) report implementation of a set of standard real-time fMRI denoising steps according to a proposed COBIDAS-style checklist (https://osf.io/kjwhf/), (b) ensure the quality of the neurofeedback signal by calculating and reporting community-informed quality metrics and applying offline control checks and (c) strive to adopt transparent principles in the form of methods and data sharing and support of open-source rtfMRI-NF software. Code and data for reproducibility, as well as an interactive environment to explore the study data, can be accessed at https://github.com/jsheunis/quality-and-denoising-in-rtfmri-nf.

The role of the subgenual anterior cingulate cortex in dorsomedial prefrontal-amygdala neural circuitry during positive-social emotion regulation

Positive-social emotions mediate one's cognitive performance, mood, well-being, and social bonds, and represent a critical variable within therapeutic settings. It has been shown that the upregulation of positive emotions in social situations is associated with increased top-down signals that stem from the prefrontal cortices (PFC) which modulate bottom-up emotional responses in the amygdala. However, it remains unclear if positive-social emotion upregulation of the amygdala occurs directly through the dorsomedial PFC (dmPFC) or indirectly linking the bilateral amygdala with the dmPFC via the subgenual anterior cingulate cortex (sgACC), an area which typically serves as a gatekeeper between cognitive and emotion networks. We performed functional MRI (fMRI) experiments with and without effortful positive-social emotion upregulation to demonstrate the functional architecture of a network involving the amygdala, the dmPFC, and the sgACC. We found that effortful positive-social emotion upregulation was associated with an increase in top-down connectivity from the dmPFC on the amygdala via both direct and indirect connections with the sgACC. Conversely, we found that emotion processes without effortful regulation increased network modulation by the sgACC and amygdala. We also found that more anxious individuals with a greater tendency to suppress emotions and intrusive thoughts, were likely to display decreased amygdala, dmPFC, and sgACC activity and stronger connectivity strength from the sgACC onto the left amygdala during effortful emotion upregulation. Analyzed brain network suggests a more general role of the sgACC in cognitive control and sheds light on neurobiological informed treatment interventions.

No time for drifting: Comparing performance and applicability of signal detrending algorithms for real-time fMRI

As a consequence of recent technological advances in the field of functional magnetic resonance imaging (fMRI), results can now be made available in real-time. This allows for novel applications such as online quality assurance of the acquisition, intra-operative fMRI, brain-computer-interfaces, and neurofeedback. To that aim, signal processing algorithms for real-time fMRI must reliably correct signal contaminations due to physiological noise, head motion, and scanner drift. The aim of this study was to compare performance of the commonly used online detrending algorithms exponential moving average (EMA), incremental general linear model (iGLM) and sliding window iGLM (iGLMwindow). For comparison, we also included offline detrending algorithms (i.e., MATLAB's and SPM8's native detrending functions). Additionally, we optimized the EMA control parameter, by assessing the algorithm's performance on a simulated data set with an exhaustive set of realistic experimental design parameters. First, we optimized the free parameters of the online and offline detrending algorithms. Next, using simulated data, we systematically compared the performance of the algorithms with respect to varying levels of Gaussian and colored noise, linear and non-linear drifts, spikes, and step function artifacts. Additionally, using in vivo data from an actual rt-fMRI experiment, we validated our results in a post hoc offline comparison of the different detrending algorithms. Quantitative measures show that all algorithms perform well, even though they are differently affected by the different artifact types. The iGLM approach outperforms the other online algorithms and achieves online detrending performance that is as good as that of offline procedures. These results may guide developers and users of real-time fMRI analyses tools to best account for the problem of signal drifts in real-time fMRI.

Brain networks for engaging oneself in positive-social emotion regulation

Positive emotions facilitate cognitive performance, and their absence is associated with burdening psychiatric disorders. However, the brain networks regulating positive emotions are not well understood, especially with regard to engaging oneself in positive-social situations. Here we report convergent evidence from a multimodal approach that includes functional magnetic resonance imaging (fMRI) brain activations, meta-analytic functional characterization, Bayesian model-driven analysis of effective brain connectivity, and personality questionnaires to identify the brain networks mediating the cognitive up-regulation of positive-social emotions. Our comprehensive approach revealed that engaging in positive-social emotion regulation with a self-referential first-person perspective is characterized by dynamic interactions between functionally specialized prefrontal cortex (PFC) areas, the temporoparietal junction (TPJ) and the amygdala. Increased top-down connectivity from the superior frontal gyrus (SFG) controls affective valuation in the ventromedial and dorsomedial PFC, self-referential processes in the TPJ, and modulate emotional responses in the amygdala via the ventromedial PFC. Understanding the brain networks engaged in the regulation of positive-social emotions that involve a first-person perspective is important as they are known to constitute an effective strategy in therapeutic settings.