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Jonathan C.W. Brooks

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13 papers

1 author row

YNIMG Journal 2023 Journal Article

Reliability of resting-state functional connectivity in the human spinal cord: Assessing the impact of distinct noise sources

Merve Kaptan
Ulrike Horn
S. Johanna Vannesjo
Toralf Mildner
Nikolaus Weiskopf
Jürgen Finsterbusch
Jonathan C.W. Brooks
Falk Eippert

The investigation of spontaneous fluctuations of the blood-oxygen-level-dependent (BOLD) signal has recently been extended from the brain to the spinal cord, where it has stimulated interest from a clinical perspective. A number of resting-state functional magnetic resonance imaging (fMRI) studies have demonstrated robust functional connectivity between the time series of BOLD fluctuations in bilateral dorsal horns and between those in bilateral ventral horns, in line with the functional neuroanatomy of the spinal cord. A necessary step prior to extension to clinical studies is assessing the reliability of such resting-state signals, which we aimed to do here in a group of 45 healthy young adults at the clinically prevalent field strength of 3T. When investigating connectivity in the entire cervical spinal cord, we observed fair to good reliability for dorsal-dorsal and ventral-ventral connectivity, whereas reliability was poor for within- and between-hemicord dorsal-ventral connectivity. Considering how prone spinal cord fMRI is to noise, we extensively investigated the impact of distinct noise sources and made two crucial observations: removal of physiological noise led to a reduction in functional connectivity strength and reliability - due to the removal of stable and participant-specific noise patterns - whereas removal of thermal noise considerably increased the detectability of functional connectivity without a clear influence on reliability. Finally, we also assessed connectivity within spinal cord segments and observed that while the pattern of connectivity was similar to that of whole cervical cord, reliability at the level of single segments was consistently poor. Taken together, our results demonstrate the presence of reliable resting-state functional connectivity in the human spinal cord even after thoroughly accounting for physiological and thermal noise, but at the same time urge caution if focal changes in connectivity (e.g. due to segmental lesions) are to be studied, especially in a longitudinal manner.

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YNICL Journal 2021 Journal Article

Disrupted brain connectivity in children treated with therapeutic hypothermia for neonatal encephalopathy

Arthur P.C. Spencer
Jonathan C.W. Brooks
Naoki Masuda
Hollie Byrne
Richard Lee-Kelland
Sally Jary
Marianne Thoresen
James Tonks

Therapeutic hypothermia following neonatal encephalopathy due to birth asphyxia reduces death and cerebral palsy. However, school-age children without cerebral palsy treated with therapeutic hypothermia for neonatal encephalopathy still have reduced performance on cognitive and motor tests, attention difficulties, slower reaction times and reduced visuo-spatial processing abilities compared to typically developing controls. We acquired diffusion-weighted imaging data from school-age children without cerebral palsy treated with therapeutic hypothermia for neonatal encephalopathy at birth, and a matched control group. Voxelwise analysis (33 cases, 36 controls) confirmed reduced fractional anisotropy in widespread areas of white matter in cases, particularly in the fornix, corpus callosum, anterior and posterior limbs of the internal capsule bilaterally and cingulum bilaterally. In structural brain networks constructed using probabilistic tractography (22 cases, 32 controls), graph-theoretic measures of strength, local and global efficiency, clustering coefficient and characteristic path length were found to correlate with IQ in cases but not controls. Network-based statistic analysis implicated brain regions involved in visuo-spatial processing and attention, aligning with previous behavioural findings. These included the precuneus, thalamus, left superior parietal gyrus and left inferior temporal gyrus. Our findings demonstrate that, despite the manifest successes of therapeutic hypothermia, brain development is impaired in these children.

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YNICL Journal 2021 Journal Article

Motor function and white matter connectivity in children cooled for neonatal encephalopathy

Arthur P.C. Spencer
Jonathan C.W. Brooks
Naoki Masuda
Hollie Byrne
Richard Lee-Kelland
Sally Jary
Marianne Thoresen
Marc Goodfellow

Therapeutic hypothermia reduces the incidence of severe motor disability, such as cerebral palsy, following neonatal hypoxic-ischaemic encephalopathy. However, cooled children without cerebral palsy at school-age demonstrate motor deficits and altered white matter connectivity. In this study, we used diffusion-weighted imaging to investigate the relationship between white matter connectivity and motor performance, measured using the Movement Assessment Battery for Children-2, in children aged 6-8 years treated with therapeutic hypothermia for neonatal hypoxic-ischaemic encephalopathy at birth, who did not develop cerebral palsy (cases), and matched typically developing controls. Correlations between total motor scores and diffusion properties in major white matter tracts were assessed in 33 cases and 36 controls. In cases, significant correlations (FDR-corrected P < 0.05) were found in the anterior thalamic radiation bilaterally (left: r = 0.513; right: r = 0.488), the cingulate gyrus part of the left cingulum (r = 0.588), the hippocampal part of the left cingulum (r = 0.541), and the inferior fronto-occipital fasciculus bilaterally (left: r = 0.445; right: r = 0.494). No significant correlations were found in controls. We then constructed structural connectivity networks, for 22 cases and 32 controls, in which nodes represent brain regions and edges were determined by probabilistic tractography and weighted by fractional anisotropy. Analysis of whole-brain network metrics revealed correlations (FDR-corrected P < 0.05), in cases, between total motor scores and average node strength (r = 0.571), local efficiency (r = 0.664), global efficiency (r = 0.677), clustering coefficient (r = 0.608), and characteristic path length (r = -0.652). No significant correlations were found in controls. We then investigated edge-level association with motor function using the network-based statistic. This revealed subnetworks which exhibited group differences in the association between motor outcome and edge weights, for total motor scores (P = 0.0109) as well as for balance (P = 0.0245) and manual dexterity (P = 0.0233) domain scores. All three of these subnetworks comprised numerous frontal lobe regions known to be associated with motor function, including the superior frontal gyrus and middle frontal gyrus. The subnetwork associated with total motor scores was highly left-lateralised. These findings demonstrate an association between impaired motor function and brain organisation in school-age children treated with therapeutic hypothermia for neonatal hypoxic-ischaemic encephalopathy.

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YNIMG Journal 2021 Journal Article

Parallel cortical-brainstem pathways to attentional analgesia

Valeria Oliva
Rob Gregory
Wendy-Elizabeth Davies
Lee Harrison
Rosalyn Moran
Anthony E. Pickering
Jonathan C.W. Brooks

Pain demands attention, yet pain can be reduced by focusing attention elsewhere. The neural processes involved in this robust psychophysical phenomenon, attentional analgesia, are still being defined. Our previous fMRI study linked activity in the brainstem triad of locus coeruleus (LC), rostral ventromedial medulla (RVM) and periaqueductal grey (PAG) with attentional analgesia. Here we identify and model the functional interactions between these regions and the cortex in healthy human subjects (n = 57), who received painful thermal stimuli whilst simultaneously performing a visual attention task. RVM activity encoded pain intensity while contralateral LC activity correlated with attentional analgesia. Psycho-Physiological Interaction analysis and Dynamic Causal Modelling identified two parallel paths between forebrain and brainstem. These connections are modulated by attentional demand: a bidirectional anterior cingulate cortex (ACC) - right-LC loop, and a top-down influence of task on ACC-PAG-RVM. By recruiting discrete brainstem circuits, the ACC is able to modulate nociceptive input to reduce pain in situations of conflicting attentional demand.

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YNIMG Journal 2019 Journal Article

Keeping track of ‘alternative facts’: The neural correlates of processing misinformation corrections

Andrew Gordon
Susanne Quadflieg
Jonathan C.W. Brooks
Ullrich K.H. Ecker
Stephan Lewandowsky

Upon receiving a correction, initially presented misinformation often continues to influence people's judgment and reasoning. Whereas some researchers believe that this so-called continued influence effect of misinformation (CIEM) simply arises from the insufficient encoding and integration of corrective claims, others assume that it arises from a competition between the correct information and the initial misinformation in memory. To examine these possibilities, we conducted two functional magnetic resonance imaging (fMRI) studies. In each study, participants were asked to (a) read a series of brief news reports that contained confirmations or corrections of prior information and (b) evaluate whether subsequently presented memory probes matched the reports' correct facts rather than the initial misinformation. Both studies revealed that following correction-containing news reports, participants struggled to refute mismatching memory probes, especially when they referred to initial misinformation (as opposed to mismatching probes with novel information). We found little evidence, however, that the encoding of confirmations and corrections produced systematic neural processing differences indicative of distinct encoding strategies. Instead, we discovered that following corrections, participants exhibited increased activity in the left angular gyrus and the bilateral precuneus in response to mismatching memory probes that contained prior misinformation, compared to novel mismatch probes. These findings favour the notion that people's susceptibility to the CIEM arises from the concurrent retention of both correct and incorrect information in memory.

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YNIMG Journal 2017 Journal Article

Denoising spinal cord fMRI data: Approaches to acquisition and analysis

Falk Eippert
Yazhuo Kong
Mark Jenkinson
Irene Tracey
Jonathan C.W. Brooks

Functional magnetic resonance imaging (fMRI) of the human spinal cord is a difficult endeavour due to the cord's small cross-sectional diameter, signal drop-out as well as image distortion due to magnetic field inhomogeneity, and the confounding influence of physiological noise from cardiac and respiratory sources. Nevertheless, there is great interest in spinal fMRI due to the spinal cord's role as the principal sensorimotor interface between the brain and the body and its involvement in a variety of sensory and motor pathologies. In this review, we give an overview of the various methods that have been used to address the technical challenges in spinal fMRI, with a focus on reducing the impact of physiological noise. We start out by describing acquisition methods that have been tailored to the special needs of spinal fMRI and aim to increase the signal-to-noise ratio and reduce distortion in obtained images. Following this, we concentrate on image processing and analysis approaches that address the detrimental effects of noise. While these include variations of standard pre-processing methods such as motion correction and spatial filtering, the main focus lies on denoising techniques that can be applied to task-based as well as resting-state data sets. We review both model-based approaches that rely on externally acquired respiratory and cardiac signals as well as data-driven approaches that estimate and correct for noise using the data themselves. We conclude with an outlook on techniques that have been successfully applied for noise reduction in brain imaging and whose use might be beneficial for fMRI of the human spinal cord.

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YNIMG Journal 2017 Journal Article

Investigating resting-state functional connectivity in the cervical spinal cord at 3 T

Falk Eippert
Yazhuo Kong
Anderson M. Winkler
Jesper L. Andersson
Jürgen Finsterbusch
Christian Büchel
Jonathan C.W. Brooks
Irene Tracey

The study of spontaneous fluctuations in the blood-oxygen-level-dependent (BOLD) signal has recently been extended from the brain to the spinal cord. Two ultra-high field functional magnetic resonance imaging (fMRI) studies in humans have provided evidence for reproducible resting-state connectivity between the dorsal horns as well as between the ventral horns, and a study in non-human primates has shown that these resting-state signals are impacted by spinal cord injury. As these studies were carried out at ultra-high field strengths using region-of-interest (ROI) based analyses, we investigated whether such resting-state signals could also be observed at the clinically more prevalent field strength of 3T. In a reanalysis of a sample of 20 healthy human participants who underwent a resting-state fMRI acquisition of the cervical spinal cord, we were able to observe significant dorsal horn connectivity as well as ventral horn connectivity, but no consistent effects for connectivity between dorsal and ventral horns, thus replicating the human 7T results. These effects were not only observable when averaging along the acquired length of the spinal cord, but also when we examined each of the acquired spinal segments separately, which showed similar patterns of connectivity. Finally, we investigated the robustness of these resting-state signals against variations in the analysis pipeline by varying the type of ROI creation, temporal filtering, nuisance regression and connectivity metric. We observed that – apart from the effects of band-pass filtering – ventral horn connectivity showed excellent robustness, whereas dorsal horn connectivity showed moderate robustness. Together, our results provide evidence that spinal cord resting-state connectivity is a robust and spatially consistent phenomenon that could be a valuable tool for investigating the effects of pathology, disease progression, and treatment response in neurological conditions with a spinal component, such as spinal cord injury.

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YNIMG Journal 2014 Journal Article

Optimizing RetroICor and RetroKCor corrections for multi-shot 3D FMRI acquisitions

Rob H.N. Tijssen
Mark Jenkinson
Jonathan C.W. Brooks
Peter Jezzard
Karla L. Miller

Physiological noise, if unaccounted for, can drastically reduce the statistical significance of detected activation in FMRI. In this paper, we systematically optimize physiological noise regressions for multi-shot 3D FMRI data. First, we investigate whether 3D FMRI data are best corrected in image space (RetroICor) or k-space (RetroKCor), in which each k-space segment can be assigned its unique physiological phase. In addition, the optimal regressor set is determined using the Bayesian Information Criterion (BIC) for a variety of 3D acquisitions corresponding to different image contrasts and k-space readouts. Our simulations and experiments indicate that: (a) k-space corrections are more robust when performed on real/imaginary than magnitude/phase data; (b) k-space corrections do not outperform image-space corrections, despite the ability to synchronize physiological phase to acquisition time more accurately; and (c) the optimal model varied considerably between the various acquisition techniques. These results suggest the use of a tailored set of volume-wide regressors, determined by BIC or other selection criteria, that achieves optimal balance between variance reduction and potential over-fitting.

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YNIMG Journal 2012 Journal Article

Assessment of physiological noise modelling methods for functional imaging of the spinal cord

Yazhuo Kong
Mark Jenkinson
Jesper Andersson
Irene Tracey
Jonathan C.W. Brooks

The spinal cord is the main pathway for information between the central and the peripheral nervous systems. Non-invasive functional MRI offers the possibility of studying spinal cord function and central sensitisation processes. However, imaging neural activity in the spinal cord is more difficult than in the brain. A significant challenge when dealing with such data is the influence of physiological noise (primarily cardiac and respiratory), and currently there is no standard approach to account for these effects. We have previously studied the various sources of physiological noise for spinal cord fMRI at 1. 5T and proposed a physiological noise model (PNM) (Brooks et al. , 2008). An alternative de-noising strategy, selective averaging filter (SAF), was proposed by Deckers et al. (2006). In this study we reviewed and implemented published physiological noise correction methods at higher field (3T) and aimed to find the optimal models for gradient-echo-based BOLD acquisitions. Two general techniques were compared: physiological noise model (PNM) and selective averaging filter (SAF), along with regressors designed to account for specific signal compartments and physiological processes: cerebrospinal fluid (CSF), motion correction (MC) parameters, heart rate (HR), respiration volume per time (RVT), and the associated cardiac and respiratory response functions. Functional responses were recorded from the cervical spinal cord of 18 healthy subjects in response to noxious thermal and non-noxious punctate stimulation. The various combinations of models and regressors were compared in three ways: the model fit residuals, regression model F-tests and the number of activated voxels. The PNM was found to outperform SAF in all three tests. Furthermore, inclusion of the CSF regressor was crucial as it explained a significant amount of signal variance in the cord and increased the number of active cord voxels. Whilst HR, RVT and MC explained additional signal (noise) variance, they were also found (in particular HR and RVT) to have a negative impact on the parameter estimates (of interest) — as they may be correlated with task conditions e. g. noxious thermal stimuli. Convolution with previously published cardiac and respiratory impulse response functions was not found to be beneficial. The other novel aspect of current study is the investigation of the influence of pre-whitening together with PNM regressors on spinal fMRI data. Pre-whitening was found to reduce non-white noise, which was not accounted for by physiological noise correction, and decrease false positive detection rates.

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YNIMG Journal 2012 Journal Article

Identification and characterisation of midbrain nuclei using optimised functional magnetic resonance imaging

Eve H. Limbrick-Oldfield
Jonathan C.W. Brooks
Richard J.S. Wise
Francesco Padormo
Jo V. Hajnal
Christian F. Beckmann
Mark A. Ungless

Localising activity in the human midbrain with conventional functional MRI (fMRI) is challenging because the midbrain nuclei are small and located in an area that is prone to physiological artefacts. Here we present a replicable and automated method to improve the detection and localisation of midbrain fMRI signals. We designed a visual fMRI task that was predicted would activate the superior colliculi (SC) bilaterally. A limited number of coronal slices were scanned, orientated along the long axis of the brainstem, whilst simultaneously recording cardiac and respiratory traces. A novel anatomical registration pathway was used to optimise the localisation of the small midbrain nuclei in stereotactic space. Two additional structural scans were used to improve registration between functional and structural T1-weighted images: an echo-planar image (EPI) that matched the functional data but had whole-brain coverage, and a whole-brain T2-weighted image. This pathway was compared to conventional registration pathways, and was shown to significantly improve midbrain registration. To reduce the physiological artefacts in the functional data, we estimated and removed structured noise using a modified version of a previously described physiological noise model (PNM). Whereas a conventional analysis revealed only unilateral SC activity, the PNM analysis revealed the predicted bilateral activity. We demonstrate that these methods improve the measurement of a biologically plausible fMRI signal. Moreover they could be used to investigate the function of other midbrain nuclei.

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YNIMG Journal 2008 Journal Article

Physiological noise modelling for spinal functional magnetic resonance imaging studies

Jonathan C.W. Brooks
Christian F. Beckmann
Karla L. Miller
Richard G. Wise
Carlo A. Porro
Irene Tracey
Mark Jenkinson

Spinal cord functional imaging allows assessment of activity in primary synaptic connections made by sensory neurons relaying information about the state of the body. However, reported human data based on gradient-echo techniques have been largely inconsistent, with no clear patterns of activation emerging. One reason for this variability is the influence of physiological noise, which is typically not corrected for. By acquiring single-slice resting data from the spinal cord with a conventional gradient-echo EPI pulse sequence at TR=200 ms (critically sampled) and TR=3 s (under-sampled), we have characterised various sources of physiological noise. In 8 healthy subjects, the presence of physiologically dependent signal was explored using probabilistic independent component analysis (PICA). Based on the insights provided by PICA, we defined a new physiological noise model (PNM) based on retrospective image correction (RETROICOR), which uses independent physiological measurements taken from the subject to model sources of noise. Statistical significance of individual components included in the PNM was assessed by F-tests, which demonstrated that the optimal PNM included cardiac, respiratory, interaction and low-frequency regressors. In a group of 10 healthy subjects, activation data were acquired from the cervical spinal region (T1 to C5) during painful thermal stimulation of the right and left hands. The improvement obtained when using a PNM in estimating spinal cord activation was reflected in a reduction of false-positive activation (active voxels in the CSF space surrounding the cord), when compared to conventional GLM modelling without a PNM.

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YNIMG Journal 2005 Journal Article

Quantitative assessment of the reproducibility of functional activation measured with BOLD and MR perfusion imaging: Implications for clinical trial design

Teddy Tjandra
Jonathan C.W. Brooks
Patricia Figueiredo
Richard Wise
Paul M. Matthews
Irene Tracey

BOLD contrast is the most commonly used functional MRI method for studies of brain activity. However, the underlying physiological processes giving rise to measured BOLD signal changes (which include contribution from changes in cerebral blood flow (CBF), cerebral blood volume (CBV) and cerebral metabolic rate of oxygen consumption (CMRO2)) vary substantially between sessions and subjects. To determine whether direct CBF measurement is a more reliable technique, we compared the localisation of activation and reproducibility of relative signal change measured by optimised BOLD versus CBF measured using the arterial spin labelling (ASL) technique. Data were collected within the primary sensorimotor cortex in normal healthy controls performing a simple finger-tapping task over three imaging sessions (two on same day and one on a different day). The displacement between the foci of BOLD and CBF activation was less than the linear dimension of one voxel (2. 4 mm), however, BOLD activation was significantly closer to the nearest draining vein compared to CBF activation (P = 0. 030). For the relative signal change measurement, we found that CBF has a lower inter-subject variation than BOLD (P < 0. 05), enabling a smaller sample size for any given effect size, although the intra-subject variation across sessions for CBF was not significantly different from BOLD. BOLD imaging provides the optimal contrast for exploratory brain activation mapping, however, for a single time-point group study, CBF has reduced variance. In addition, the reduction of variance over time using CBF measurements (non-significant) suggests it could potentially provide a more useful approach when assessing longitudinal activation changes.

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YNIMG Journal 2002 Journal Article

fMRI of Thermal Pain: Effects of Stimulus Laterality and Attention

Jonathan C.W. Brooks
Turo J. Nurmikko
William E. Bimson
Krish D. Singh
Neil Roberts

Brain activity was studied by fMRI in 18 healthy subjects during stimulation of the thenar eminence of the hand with either warm (nonpainful, 40°C) or hot (painful, 46–49°C) stimuli using a contact thermode. Experiments were performed on the right and left hand independently and with two attentional contexts: subjects either attended to pain or attended to a visual global motion discrimination task (to distract them from pain). Group analysis demonstrated that attended warm stimulation of the right hand did not produce any significantly activated clusters. Painful thermal stimulation of either hand elicited significant activity over a large network of brain regions, including insula, inferior frontal gyrus, cingulate gyrus, secondary somatosensory cortex, cerebellum, and medial frontal gyrus (corrected P < 0. 05). Insula activity was distributed along its anterior–posterior axis and depended on the hand stimulated and attentional context. In particular, activity within the posterior insula was contralateral to the site of stimulation, tested using regions of interest (ROI) analysis: significant side × site interaction (P = 0. 001). With attention diverted from the painful stimulus bilateral anterior insula activity moved posteriorly to midinsula and decreased in extent (ROI analysis: significant main effect of attention (P = 0. 03)). The role of the insula in thermosensation and attention is discussed.

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