Functionnectome as a framework to analyse the contribution of brain circuits to fMRI.

In recent years, the field of functional neuroimaging has moved away from a pure localisationist approach of isolated functional brain regions to a more integrated view of these regions within functional networks. However, the methods used to investigate functional networks rely on local signals in grey matter and are limited in identifying anatomical circuitries supporting the interaction between brain regions. Mapping the brain circuits mediating the functional signal between brain regions would propel our understanding of the brain's functional signatures and dysfunctions. We developed a method to unravel the relationship between brain circuits and functions: The Functionnectome. The Functionnectome combines the functional signal from fMRI with white matter circuits' anatomy to unlock and chart the first maps of functional white matter. To showcase this method's versatility, we provide the first functional white matter maps revealing the joint contribution of connected areas to motor, working memory, and language functions. The Functionnectome comes with an open-source companion software and opens new avenues into studying functional networks by applying the method to already existing datasets and beyond task fMRI.

Resting state fMRI scanner instabilities revealed by longitudinal phantom scans in a multi-center study.

Quality assurance (QA) is crucial in longitudinal and/or multi-site studies, which involve the collection of data from a group of subjects over time and/or at different locations. It is important to regularly monitor the performance of the scanners over time and at different locations to detect and control for intrinsic differences (e.g., due to manufacturers) and changes in scanner performance (e.g., due to gradual component aging, software and/or hardware upgrades, etc.). As part of the Ontario Neurodegenerative Disease Research Initiative (ONDRI) and the Canadian Biomarker Integration Network in Depression (CAN-BIND), QA phantom scans were conducted approximately monthly for three to four years at 13 sites across Canada with 3T research MRI scanners. QA parameters were calculated for each scan using the functional Biomarker Imaging Research Network's (fBIRN) QA phantom and pipeline to capture between- and within-scanner variability. We also describe a QA protocol to measure the full-width-at-half-maximum (FWHM) of slice-wise point spread functions (PSF), used in conjunction with the fBIRN QA parameters. Variations in image resolution measured by the FWHM are a primary source of variance over time for many sites, as well as between sites and between manufacturers. We also identify an unexpected range of instabilities affecting individual slices in a number of scanners, which may amount to a substantial contribution of unexplained signal variance to their data. Finally, we identify a preliminary preprocessing approach to reduce this variance and/or alleviate the slice anomalies, and in a small human data set show that this change in preprocessing can have a significant impact on seed-based connectivity measurements for some individual subjects. We expect that other fMRI centres will find this approach to identifying and controlling scanner instabilities useful in similar studies.

Brainwide functional networks associated with anatomically- and functionally-defined hippocampal subfields using ultrahigh-resolution fMRI.

The hippocampus is critical for learning and memory and may be separated into anatomically-defined hippocampal subfields (aHPSFs). Hippocampal functional networks, particularly during resting state, are generally analyzed using aHPSFs as seed regions, with the underlying assumption that the function within a subfield is homogeneous, yet heterogeneous between subfields. However, several prior studies have observed similar resting-state functional connectivity (FC) profiles between aHPSFs. Alternatively, data-driven approaches investigate hippocampal functional organization without a priori assumptions. However, insufficient spatial resolution may result in a number of caveats concerning the reliability of the results. Hence, we developed a functional Magnetic Resonance Imaging (fMRI) sequence on a 7 T MR scanner achieving 0.94 mm isotropic resolution with a TR of 2 s and brain-wide coverage to (1) investigate the functional organization within hippocampus at rest, and (2) compare the brain-wide FC associated with fine-grained aHPSFs and functionally-defined hippocampal subfields (fHPSFs). This study showed that fHPSFs were arranged along the longitudinal axis that were not comparable to the lamellar structures of aHPSFs. For brain-wide FC, the fHPSFs rather than aHPSFs revealed that a number of fHPSFs connected specifically with some of the functional networks. Different functional networks also showed preferential connections with different portions of hippocampal subfields.

Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity.

Functional neuroimaging using MRI relies on measurements of blood oxygen level-dependent (BOLD) signals from which inferences are made about the underlying neuronal activity. This is possible because neuronal activity elicits increases in blood flow via neurovascular coupling, which gives rise to the BOLD signal. Hence, an accurate interpretation of what BOLD signals mean in terms of neural activity depends on a full understanding of the mechanisms that underlie the measured signal, including neurovascular and neurometabolic coupling, the contribution of different cell types to local signalling, and regional differences in these mechanisms. Furthermore, the contributions of systemic functions to cerebral blood flow may vary with ageing, disease and arousal states, with regard to both neuronal and vascular function. In addition, recent developments in non-invasive imaging technology, such as high-field fMRI, and comparative inter-species analysis, allow connections between non-invasive data and mechanistic knowledge gained from invasive cellular-level studies. Considered together, these factors have immense potential to improve BOLD signal interpretation and bring us closer to the ultimate purpose of decoding the mechanisms of human cognition. This theme issue covers a range of recent advances in these topics, providing a multidisciplinary scientific and technical framework for future work in the neurovascular and cognitive sciences. This article is part of the theme issue 'Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity'.

Forging a path to mesoscopic imaging success with ultra-high field functional magnetic resonance imaging.

Functional magnetic resonance imaging (fMRI) studies with ultra-high field (UHF, 7+ Tesla) technology enable the acquisition of high-resolution images. In this work, we discuss recent achievements in UHF fMRI at the mesoscopic scale, on the order of cortical columns and layers, and examine approaches to addressing common challenges. As researchers push to smaller and smaller voxel sizes, acquisition and analysis decisions have greater potential to degrade spatial accuracy, and UHF fMRI data must be carefully interpreted. We consider the impact of acquisition decisions on the spatial specificity of the MR signal with a representative dataset with 0.8 mm isotropic resolution. We illustrate the trade-offs in contrast with noise ratio and spatial specificity of different acquisition techniques and show that acquisition blurring can increase the effective voxel size by as much as 50% in some dimensions. We further describe how different sources of degradations to spatial resolution in functional data may be characterized. Finally, we emphasize that progress in UHF fMRI depends not only on scientific discovery and technical advancement, but also on informal discussions and documentation of challenges researchers face and overcome in pursuit of their goals. This article is part of the theme issue 'Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity'.

Resting-state functional brain alterations in functional dyspepsia: Protocol for a systematic review and voxel-based meta-analysis.

BACKGROUND: Functional dyspepsia (FD) is one of the most common functional gastrointestinal disorders (FGIDs) and significantly influences patients' quality of life. Many studies have found that patients with FD show significant functional abnormalities in multiple brain regions. However, these functional cerebral abnormalities are not fully consistent. This protocol aims to qualitatively and quantitatively assess and synthesize the functional cerebral abnormalities found in FD. METHODS: A systematic search will be conducted in 4 electronic databases (Medline, Web of Science, EMBASE, and the Cochrane Library) from inception to June 30, 2019, with the language restricted to English. Study selection will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Quality assessment will be performed with a custom 11-point checklist. The functional changes in brain regions and the correlations between these altered brain regions and clinical variables in patients with FD will be evaluated through qualitative review. If data are available, an Anisotropic Effect Size version of Signed Differential Mapping (AES-SDM) will be used to synthesize the brain functional alterations and clinical variables in patients with FD. RESULTS: This review and meta-analysis will qualitatively and quantitatively assess and synthesize functional cerebral abnormalities consistently found in FD. CONCLUSION: This may assist in mapping functional brain abnormalities to characterize imaging-based neural markers of FD and improve our knowledge of the pathogenesis of FD. PROSPERO REGISTRATION NUMBER: CRD42019134983 (https://www.crd.york.ac.uk/prospero/).

Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity-at Depth and in Real Time.

We propose a new paradigm for dense functional imaging of brain activity to surmount the limitations of present methodologies. We term this approach "integrated neurophotonics"; it combines recent advances in microchip-based integrated photonic and electronic circuitry with those from optogenetics. This approach has the potential to enable lens-less functional imaging from within the brain itself to achieve dense, large-scale stimulation and recording of brain activity with cellular resolution at arbitrary depths. We perform a computational study of several prototype 3D architectures for implantable probe-array modules that are designed to provide fast and dense single-cell resolution (e.g., within a 1-mm3 volume of mouse cortex comprising ∼100,000 neurons). We describe progress toward realizing integrated neurophotonic imaging modules, which can be produced en masse with current semiconductor foundry protocols for chip manufacturing. Implantation of multiple modules can cover extended brain regions.

Brain correlates of motor complexity during observed and executed actions.

Recently, cortical areas with motor properties have attracted attention widely to their involvement in both action generation and perception. Inferior frontal gyrus (IFG), ventral premotor cortex (PMv) and inferior parietal lobule (IPL), presumably consisting of motor-related areas, are of particular interest, given that they respond to motor behaviors both when they are performed and observed. Converging neuroimaging evidence has shown the functional roles of IFG, PMv and IPL in action understanding. Most studies have focused on the effects of modulations in goals and kinematics of observed actions on the brain response, but little research has explored the effects of manipulations in motor complexity. To address this, we used fNIRS to examine the brain activity in the frontal, motor, parietal and occipital regions, aiming to better understand the brain correlates involved in encoding motor complexity. Twenty-one healthy adults executed and observed two hand actions that differed in motor complexity. We found that motor complexity sensitive brain regions were present in the pars opercularis IFG/PMv, primary motor cortex (M1), IPL/supramarginal gyrus and middle occipital gyrus (MOG) during action execution, and in pars opercularis IFG/PMv and M1 during action observation. Our findings suggest that the processing of motor complexity involves not only M1 but also pars opercularis IFG, PMv and IPL, each of which plays a critical role in action perception and execution.

Multi-channel whole-head OPM-MEG: Helmet design and a comparison with a conventional system.

Magnetoencephalography (MEG) is a powerful technique for functional neuroimaging, offering a non-invasive window on brain electrophysiology. MEG systems have traditionally been based on cryogenic sensors which detect the small extracranial magnetic fields generated by synchronised current in neuronal assemblies, however, such systems have fundamental limitations. In recent years, non-cryogenic quantum-enabled sensors, called optically-pumped magnetometers (OPMs), in combination with novel techniques for accurate background magnetic field control, have promised to lift those restrictions offering an adaptable, motion-robust MEG system, with improved data quality, at reduced cost. However, OPM-MEG remains a nascent technology, and whilst viable systems exist, most employ small numbers of sensors sited above targeted brain regions. Here, building on previous work, we construct a wearable OPM-MEG system with 'whole-head' coverage based upon commercially available OPMs, and test its capabilities to measure alpha, beta and gamma oscillations. We design two methods for OPM mounting; a flexible (EEG-like) cap and rigid (additively-manufactured) helmet. Whilst both designs allow for high quality data to be collected, we argue that the rigid helmet offers a more robust option with significant advantages for reconstruction of field data into 3D images of changes in neuronal current. Using repeat measurements in two participants, we show signal detection for our device to be highly robust. Moreover, via application of source-space modelling, we show that, despite having 5 times fewer sensors, our system exhibits comparable performance to an established cryogenic MEG device. While significant challenges still remain, these developments provide further evidence that OPM-MEG is likely to facilitate a step change for functional neuroimaging.

Non-Invasive Functional-Brain-Imaging with an OPM-based Magnetoencephalography System.

A non-invasive functional-brain-imaging system based on optically-pumped-magnetometers (OPM) is presented. The OPM-based magnetoencephalography (MEG) system features 20 OPM channels conforming to the subject's scalp. We have conducted two MEG experiments on three subjects: assessment of somatosensory evoked magnetic field (SEF) and auditory evoked magnetic field (AEF) using our OPM-based MEG system and a commercial MEG system based on superconducting quantum interference devices (SQUIDs). We cross validated the robustness of our system by calculating the distance between the location of the equivalent current dipole (ECD) yielded by our OPM-based MEG system and the ECD location calculated by the commercial SQUID-based MEG system. We achieved sub-centimeter accuracy for both SEF and AEF responses in all three subjects. Due to the proximity (12 mm) of the OPM channels to the scalp, it is anticipated that future OPM-based MEG systems will offer enhanced spatial resolution as they will capture finer spatial features compared to traditional MEG systems employing SQUIDs.

Chronic low back pain and sick-leave: a functional magnetic resonance study

Abstract Background Chronic low back pain (CLBP) represents a problem in the occupational environment, often associated with disability, sick-leave demands, loss of productivity, anxiety, depression and high socioeconomic cost. The emergence of functional neuroimaging allowed new insights into brain structure and physiology in normality and chronic pain. While occupational related aspects are recognized as important risk factors for chronicity there have not been thus far evaluated by fMRI experiments. The overall objective of this study is to compare the neuronal correlates between groups of individuals CLBP with or without sick-leave demands. Methods A total of 74 individuals were divided into three groups: chronic low back pain with sick-leave demands [CLBP_L]; chronic low back pain without sick-leave demands [CLBP_NL]; individuals without pain or sick-leave demands [Control]. Functional magnetic resonance imaging was used to assess brain function during moderate acute pain stimulation task (thumb controlled pressure). Results After acute painful stimulation, a higher brain response was found in the anterior cingulate and superior and medium frontal gyrus was observed in CLBP_NL vs. CLBP_L ( p < 0,001) and increased brain response in the frontal pole and paracingulate region in control vs. CLBP_L ( p < 0.001) during acute pain stimulation. Conclusion The modulation of acute pain participates in the mechanism propagating chronic pain perception. The lower activation in the superior frontal gyrus observed in the CLBP_L group compared to CLBP_NL, reinforces the idea of an already existing activation in this area.(AU)

Small-world properties of the whole-brain functional networks in patients with obstructive sleep apnea-hypopnea syndrome.

OBJECTIVE: To explore the small-world properties of brain functional networks in patients with obstructive sleep apnea-hypopnea syndrome (OSAHS) to aid diagnosis. METHODS: A total of 29 OSAHS patients and 26 matched healthy volunteers were scanned with blood oxygen level-dependent functional magnetic resonance imaging (BOLD-fMRI) separately, and the whole brain was divided into 90 districts via automated anatomical labeling. The matrix Z was then built through a Fisher Z transformation. Two-sample t tests were applied to evaluate the changes in small-world properties in OSAHS patients compared to the control group. The properties included Eglobal, Elocal, and small-world parameters Lp, Cp, γ, λ, and σ. RESULTS: Both groups satisfied the small-world properties (σ > 1) within the sparsity range of 0.1-0.2. However, compared with the control group, the OSAHS group performed significantly lower in Cp, Elocal, and Eglobal (p < 0.05) and higher in Lp (p < 0.05). The γ, σ, and λ values were not significantly different between the two groups. CONCLUSION: Both healthy and OSAHS patients exhibited small-world properties in functional networks, but a subset of these small-world properties in OSAHS patients performed differently. These changes will not only provide a new perspective for pathophysiological mechanisms of OSAHS but will also help in understanding the disease in terms of whole-brain functional networks.

MRI-guided robotic arm drives optogenetic fMRI with concurrent Ca2+ recording.

Optical fiber-mediated optogenetic activation and neuronal Ca2+ recording in combination with fMRI provide a multi-modal fMRI platform. Here, we developed an MRI-guided robotic arm (MgRA) as a flexible positioning system with high precision to real-time assist optical fiber brain intervention for multi-modal animal fMRI. Besides the ex vivo precision evaluation, we present the highly reliable brain activity patterns in the projected basal forebrain regions upon MgRA-driven optogenetic stimulation in the lateral hypothalamus. Also, we show the step-wise optical fiber targeting thalamic nuclei and map the region-specific functional connectivity with whole-brain fMRI accompanied by simultaneous calcium recordings to specify its circuit-specificity. The MgRA also guides the real-time microinjection to specific deep brain nuclei, which is demonstrated by an Mn-enhanced MRI method. The MgRA represents a clear advantage over the standard stereotaxic-based fiber implantation and opens a broad avenue to investigate the circuit-specific functional brain mapping with the multi-modal fMRI platform.

Magnetoencephalography and the infant brain.

Magnetoencephalography (MEG) is a non-invasive neuroimaging technique that provides whole-head measures of neural activity with millisecond temporal resolution. Over the last three decades, MEG has been used for assessing brain activity, most commonly in adults. MEG has been used less often to examine neural function during early development, in large part due to the fact that infant whole-head MEG systems have only recently been developed. In this review, an overview of infant MEG studies is provided, focusing on the period from birth to three years. The advantages of MEG for measuring neural activity in infants are highlighted (See Box 1), including the ability to assess activity in brain (source) space rather than sensor space, thus allowing direct assessment of neural generator activity. Recent advances in MEG hardware and source analysis are also discussed. As the review indicates, efforts in this area demonstrate that MEG is a promising technology for studying the infant brain. As a noninvasive technology, with emerging hardware providing the necessary sensitivity, an expected deliverable is the capability for longitudinal infant MEG studies evaluating the developmental trajectory (maturation) of neural activity. It is expected that departures from neuro-typical trajectories will offer early detection and prognosis insights in infants and toddlers at-risk for neurodevelopmental disorders, thus paving the way for early targeted interventions.

Functional imaging of visual cortical layers and subplate in awake mice with optimized three-photon microscopy.

Two-photon microscopy is used to image neuronal activity, but has severe limitations for studying deeper cortical layers. Here, we developed a custom three-photon microscope optimized to image a vertical column of the cerebral cortex > 1 mm in depth in awake mice with low (<20 mW) average laser power. Our measurements of physiological responses and tissue-damage thresholds define pulse parameters and safety limits for damage-free three-photon imaging. We image functional visual responses of neurons expressing GCaMP6s across all layers of the primary visual cortex (V1) and in the subplate. These recordings reveal diverse visual selectivity in deep layers: layer 5 neurons are more broadly tuned to visual stimuli, whereas mean orientation selectivity of layer 6 neurons is slightly sharper, compared to neurons in other layers. Subplate neurons, located in the white matter below cortical layer 6 and characterized here for the first time, show low visual responsivity and broad orientation selectivity.

Feasibility of functional MRI at ultralow magnetic field via changes in cerebral blood volume.

We investigate the feasibility of performing functional MRI (fMRI) at ultralow field (ULF) with a Superconducting QUantum Interference Device (SQUID), as used for detecting magnetoencephalography (MEG) signals from the human head. While there is negligible magnetic susceptibility variation to produce blood oxygenation level-dependent (BOLD) contrast at ULF, changes in cerebral blood volume (CBV) may be a sensitive mechanism for fMRI given the five-fold spread in spin-lattice relaxation time (T1) values across the constituents of the human brain. We undertook simulations of functional signal strength for a simplified brain model involving activation of a primary cortical region in a manner consistent with a blocked task experiment. Our simulations involve measured values of T1 at ULF and experimental parameters for the performance of an upgraded ULFMRI scanner. Under ideal experimental conditions we predict a functional signal-to-noise ratio of between 3.1 and 7.1 for an imaging time of 30 min, or between 1.5 and 3.5 for a blocked task experiment lasting 7.5 min. Our simulations suggest it may be feasible to perform fMRI using a ULFMRI system designed to perform MRI and MEG in situ.

Open-field PET: Simultaneous brain functional imaging and behavioural response measurements in freely moving small animals.

A comprehensive understanding of how the brain responds to a changing environment requires techniques capable of recording functional outputs at the whole-brain level in response to external stimuli. Positron emission tomography (PET) is an exquisitely sensitive technique for imaging brain function but the need for anaesthesia to avoid motion artefacts precludes concurrent behavioural response studies. Here, we report a technique that combines motion-compensated PET with a robotically-controlled animal enclosure to enable simultaneous brain imaging and behavioural recordings in unrestrained small animals. The technique was used to measure in vivo displacement of [11C]raclopride from dopamine D2 receptors (D2R) concurrently with changes in the behaviour of awake, freely moving rats following administration of unlabelled raclopride or amphetamine. The timing and magnitude of [11C]raclopride displacement from D2R were reliably estimated and, in the case of amphetamine, these changes coincided with a marked increase in stereotyped behaviours and hyper-locomotion. The technique, therefore, allows simultaneous measurement of changes in brain function and behavioural responses to external stimuli in conscious unrestrained animals, giving rise to important applications in behavioural neuroscience.

Local hippocampal fast gamma rhythms precede brain-wide hyperemic patterns during spontaneous rodent REM sleep.

Rapid eye movement sleep (REMS) is a peculiar brain state combining the behavioral components of sleep and the electrophysiological profiles of wake. After decades of research our understanding of REMS still is precluded by the difficulty to observe its spontaneous dynamics and the lack of multimodal recording approaches to build comprehensive datasets. We used functional ultrasound (fUS) imaging concurrently with extracellular recordings of local field potentials (LFP) to reveal brain-wide spatiotemporal hemodynamics of single REMS episodes. We demonstrate for the first time the close association between global hyperemic events - largely outmatching wake levels in most brain regions - and local hippocampal theta (6-10 Hz) and fast gamma (80-110 Hz) events in the CA1 region. In particular, the power of fast gamma oscillations strongly correlated with the amplitude of subsequent vascular events. Our findings challenge our current understanding of neurovascular coupling and question the evolutionary benefit of such energy-demanding patterns in REMS function.

A 665 µW Silicon Photomultiplier-Based NIRS/EEG/EIT Monitoring ASIC for Wearable Functional Brain Imaging.

This paper presents a sub-mW ASIC for multimodal brain monitoring. The ASIC is co-integrated with electrode(s) and optodes (i.e., optical source and detector) as an active sensor to measure electroencephalography (EEG), bio-impedance (BioZ), and near-infrared spectroscopy (NIRS) on scalp. The target is to build a wearable EEG-NIRS headset for low-cost functional brain imaging. The proposed NIRS readout utilizes the near-infrared light to measure the pulse oximetry and blood oxygen saturation (SpO2). While traditional photodiodes are supported, the readout also allows the use of silicon photomultipliers (SiPMs) as optical detectors. The SiPM improves optical sensitivity while significantly reducing the average power of two LEDs to 150 µW. On circuit level, a SAR-based calibration compensates maximum 40 µA current from ambient light, while digital DC-servo loops reduces the baseline static SiPM current up to 400 µA, leading to an overall dynamic range of 87 dB. The EEG readout exhibits 720 MΩ input impedance at 50 Hz. The BioZ readout has 3 mΩ/√(Hz) impedance sensitivity by employing dynamic circuit techniques. When EEG, BioZ, and NIRS are enabled at the same time, one ASIC consumes 665 µW including the power of LEDs.

Studying brain activity in sports performance: Contributions and issues.

Understanding the interactions between brain activity and behavior comprehensively in achieving optimal exercise performance in sports is still lacking. The existent research in this area has been limited by the constraints of sports environments and the robustness of the most suitable non-invasive functional neuroimaging methods (electroencephalography, EEG and functional near-infrared spectroscopy, fNIRS) to motion artifacts and noise. However, recent advances in brain mapping technology should improve the capabilities of the future brain imaging devices to assess and monitor the level of adaptive cognitive-motor performance during exercise in sports environments. The purpose of this position manuscript is to discuss the contributions and issues in behavioral neuroscience related to brain activity measured during exercise and in various sports. A first part aims to give an overview of EEG and fNIRS neuroimaging methods assessing electrophysiological activity and hemodynamic responses of the acute and chronic relation of physical exercise on the human brain. Then, methodological issues, such as the reliability of brain data during physical exertion, key limitations and possible prospects of fNIRS and EEG methods are provided. While the use of such methods in sports environments remains scarce and limited to controlled cycling task, new generation of wearable, whole-scalp EEG and fNIRS technologies could open up a range of new applications in sports sciences for providing neuroimaging-based biomarkers (hemodynamic and/or neural electrical signals) to various types of exercise and innovative training.