Connectome Mapping Research Articles

Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics

Higher brain functions require flexible integration of information across widely distributed brain regions depending on the task context. Resting-state functional magnetic resonance imaging (fMRI) has provided substantial insight into large-scale intrinsic brain network organisation, yet the principles of rapid context-dependent reconfiguration of that intrinsic network organisation are much less understood. A major challenge for task connectome mapping is the absence of a gold standard for deriving whole-brain task-modulated functional connectivity matrices. Here, we perform biophysically realistic simulations to control the ground-truth task-modulated functional connectivity over a wide range of experimental settings. We reveal the best-performing methods for different types of task designs and their fundamental limitations. Importantly, we demonstrate that rapid (100 ms) modulations of oscillatory neuronal synchronisation can be recovered from sluggish haemodynamic fluctuations even at typically low fMRI temporal resolution (2 s). Finally, we provide practical recommendations on task design and statistical analysis to foster task connectome mapping.

Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics.

Higher brain functions require flexible integration of information across widely distributed brain regions depending on the task context. Resting-state functional magnetic resonance imaging (fMRI) has provided substantial insight into large-scale intrinsic brain network organisation, yet the principles of rapid context-dependent reconfiguration of that intrinsic network organisation are much less understood. A major challenge for task connectome mapping is the absence of a gold standard for deriving whole-brain task-modulated functional connectivity matrices. Here, we perform biophysically realistic simulations to control the ground-truth task-modulated functional connectivity over a wide range of experimental settings. We reveal the best-performing methods for different types of task designs and their fundamental limitations. Importantly, we demonstrate that rapid (100 ms) modulations of oscillatory neuronal synchronisation can be recovered from sluggish haemodynamic fluctuations even at typically low fMRI temporal resolution (2 s). Finally, we provide practical recommendations on task design and statistical analysis to foster task connectome mapping.

Release the Krakencoder: A unified brain connectome translation and fusion tool.

Brain connectivity can be estimated in many ways, depending on modality and processing strategy. Here we present the Krakencoder, a joint connectome mapping tool that simultaneously, bidirectionally translates between structural (SC) and functional connectivity (FC), and across different atlases and processing choices via a common latent representation. These mappings demonstrate unprecedented accuracy and individual-level identifiability; the mapping between SC and FC has identifiability 42-54% higher than existing models. The Krakencoder combines all connectome flavors via a shared low-dimensional latent space. This "fusion" representation i) better reflects familial relatedness, ii) preserves age- and sex-relevant information and iii) enhances cognition-relevant information. The Krakencoder can be applied without retraining to new, out-of-age-distribution data while still preserving inter-individual differences in the connectome predictions and familial relationships in the latent representations. The Krakencoder is a significant leap forward in capturing the relationship between multi-modal brain connectomes in an individualized, behaviorally- and demographically-relevant way.

Brain Connectivity Networks Constructed Using MRI for Predicting Patterns of Atrophy Progression in Parkinson Disease.

Background Whether connectome mapping of structural and functional connectivity across the brain could be used to predict patterns of atrophy progression in patients with mild Parkinson disease (PD) has not been well studied. Purpose To assess the structural and functional connectivity of brain regions in healthy controls and its relationship with the spread of gray matter (GM) atrophy in patients with mild PD. Materials and Methods This prospective study included participants with mild PD and controls recruited from a single center between January 2012 and December 2023. Participants with PD underwent three-dimensional T1-weighted brain MRI, and the extent of regional GM atrophy was determined at baseline and every year for 3 years. The structural and functional brain connectome was constructed using diffusion tensor imaging and resting-state functional MRI in healthy controls. Disease exposure (DE) indexes-indexes of the pathology of each brain region-were defined as a function of the structural or functional connectivity of all the connected regions in the healthy connectome and the severity of atrophy of the connected regions in participants with PD. Partial correlations were tested between structural and functional DE indexes of each GM region at 1- or 2-year follow-up and atrophy progression at 2- or 3-year follow-up. Prediction models of atrophy at 2- or 3-year follow-up were constructed using exhaustive feature selection. Results A total of 86 participants with mild PD (mean age at MRI, 60 years ± 8 [SD]; 48 male) and 60 healthy controls (mean age at MRI, 62 years ± 9; 31 female) were included. DE indexes at 1 and 2 years were correlated with atrophy at 2 and 3 years (r range, 0.22-0.33; P value range, .002-.04). Models including DE indexes predicted GM atrophy accumulation over 3 years in the right caudate nucleus and some frontal, parietal, and temporal brain regions (R2 range, 0.40-0.61; all P < .001). Conclusion The structural and functional organization of the brain connectome plays a role in atrophy progression in the early stages of PD. © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Yamada in this issue.

Identification and Connectomic Profiling of Concussion Using Bayesian Machine Learning.

Accurate early diagnosis of concussion is useful to prevent sequelae and improve neurocognitive outcomes. Early after head impact, concussion diagnosis may be doubtful in persons whose neurological, neuroradiological, and/or neurocognitive examinations are equivocal. Such individuals can benefit from novel accurate assessments that complement clinical diagnostics. We introduce a Bayesian machine learning classifier to identify concussion through cortico-cortical connectome mapping from magnetic resonance imaging in persons with quasi-normal cognition and without neuroradiological findings. Classifier features are generated from connectivity matrices specifying the mean fractional anisotropy of white matter connections linking brain structures. Each connection's saliency to classification was quantified by training individual classifier instantiations using a single feature type. The classifier was tested on a discovery sample of 92 healthy controls (HCs; 26 females, age μ ± σ: 39.8 ± 15.5 years) and 471 adult mTBI patients (158 females, age μ ± σ: 38.4 ± 5.9 years). Results were replicated in an independent validation sample of 256 HCs (149 females, age μ ± σ: 55.3 ± 12.1 years) and 126 patients with concussion (46 females, age μ ± σ: 39.0 ± 17.7 years). Classifier accuracy exceeds 99% in both samples, suggesting robust generalizability to new samples. Notably, 13 bilateral cortico-cortical connection pairs predict diagnostic status with accuracy exceeding 99% in both discovery and validation samples. Many such connection pairs are between prefrontal cortex structures, fronto-limbic and fronto-subcortical structures, and occipito-temporal structures in the ventral ("what") visual stream. This and related connectivity form a highly salient network of brain connections that is particularly vulnerable to concussion. Because these connections are important in mediating cognitive control, memory, and attention, our findings explain the high frequency of cognitive disturbances after concussion. Our classifier was trained and validated on concussed participants with cognitive profiles very similar to those of HCs. This suggests that the classifier can complement current diagnostics by providing independent information in clinical contexts where patients have quasi-normal cognition but where concussion diagnosis stands to benefit from additional evidence.

Differential tractography and whole brain connectometry in primary motor area gliomas resection: A feasibility study

ObjectiveEstablish the evolution of the connectome before and after resection of motor area glioma using a comparison of connectome maps and high-definition differential tractography (DifT). MethodsDifT was done using normalized quantitative anisotropy (NQA) with DSI Studio. The quantitative analysis involved obtaining mean NQA and fractional anisotropy (FA) values for the disrupted pathways tracing the corticospinal tract (CST), and white fiber network changes over time. ResultsWe described the baseline tractography, DifT, and white matter network changes from two patients who underwent resection of an oligodendroglioma (Case 1) and an IDH mutant astrocytoma, grade 4 (Case 2). Case 1. There was a slight decrease in the diffusion signal of the compromised CST in the immediate postop. The NQA and FA values increased at the 1-year follow-up (0.18 vs. 0.32 and 0.35 vs. 0.44, respectively). Case 2. There was an important decrease in the immediate postop, followed by an increase in the follow-up. In the 1-year follow-up, the patient presented with radiation necrosis and tumor recurrence, increasing NQA from 0.18 in the preop to 0.29. Fiber network analysis: whole-brain connectome comparison demonstrated no significant changes in the immediate postop. However, in the 1-year follow up there was a notorious reorganization of the fibers in both cases, showing the decreased density of connections. ConclusionsConnectome studies and DifT constitute new potential tools to predict early reorganization changes in a patient’s networks, showing the brain plasticity capacity, and helping to establish timelines for the progression of the tumor and treatment-induced changes.

Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system.

Achieving uniform optical resolution for a large tissue sample is a major challenge for deep imaging. For conventional tissueclearing methods, loss of resolution and quality in deep regions is inevitable due to limited transparency. Here we describe the Transparent Embedding Solvent System (TESOS) method, which combines tissue clearing, transparent embedding, sectioning and block-face imaging. We used TESOS to acquire volumetric images of uniform resolution for an adult mouse whole-body sample. The TESOS method is highly versatile and can be combined with different microscopy systems to achieve uniformly high resolution. With a light sheet microscope, we imaged the whole body of an adult mouse, including skin, at a uniform 0.8 × 0.8 × 3.5 μm3 voxel resolution within 120 h. With a confocal microscope and a 40×/1.3 numerical aperture objective, we achieved a uniform sub-micron resolution in the whole sample to reveal a complete projection of individual nerve axons within the central or peripheral nervous system. Furthermore, TESOS allowed the first mesoscale connectome mapping of individual sensory neuron axons spanning 5 cm from adult mouse digits to the spinal cord at a uniform sub-micron resolution.

Connectomes for 40,000 UK Biobank participants: A multi-modal, multi-scale brain network resource

We mapped functional and structural brain networks for more than 40,000 UK Biobank participants. Structural connectivity was estimated with tractography and diffusion MRI. Resting-state functional MRI was used to infer regional functional connectivity. We provide high-quality structural and functional connectomes for multiple parcellation granularities, several alternative measures of interregional connectivity, and a variety of common data pre-processing techniques, yielding more than one million connectomes in total and requiring more than 200,000 h of compute time. For a single subject, we provide 28 out-of-the-box versions of structural and functional brain networks, allowing users to select, e.g., the parcellation and connectivity measure that best suit their research goals. Furthermore, we provide code and intermediate data for the time-efficient reconstruction of more than 1000 different versions of a subject’s connectome based on an array of methodological choices. All connectomes are available via the UK Biobank data-sharing platform and our connectome mapping pipelines are openly available. In this report, we describe our connectome resource in detail for users, outline key considerations in developing an efficient pipeline to map an unprecedented number of connectomes, and report on the quality control procedures that were completed to ensure connectome reliability and accuracy. We demonstrate that our structural and functional connectivity matrices meet a number of quality control checks and replicate previously established findings in network neuroscience. We envisage that our resource will enable new studies of the human connectome in health, disease, and aging at an unprecedented scale.

Evaluation of tractogram filtering methods using human-like connectome phantoms

Tractography algorithms are prone to reconstructing spurious connections. The set of streamlines generated with tractography can be post-processed to retain the streamlines that are most biologically plausible. Several microstructure-informed filtering algorithms are available for this purpose, however, the comparative performance of these methods has not been extensively evaluated. In this study, we aim to evaluate streamline filtering and post-processing algorithms using simulated connectome phantoms. We first establish a framework for generating connectome phantoms featuring brain-like white matter fiber architectures. We then use our phantoms to systematically evaluate the performance of a range of streamline filtering algorithms, including SIFT, COMMIT, and LiFE. We find that all filtering methods successfully improve connectome accuracy, although filter performance depends on the complexity of the underlying white matter fiber architecture. Filtering algorithms can markedly improve tractography accuracy for simple tubular fiber bundles (F-measure deterministic– unfiltered: 0.49 and best filter: 0.72; F-measure probabilistic– unfiltered: 0.37 and best filter: 0.81), but for more complex brain-like fiber architectures, the improvement is modest (F-measure deterministic– unfiltered: 0.53 and best filter: 0.54; F-measure probabilistic– unfiltered: 0.46 and best filter: 0.50). Overall, filtering algorithms have the potential to improve the accuracy of connectome mapping pipelines, particularly for weighted connectomes and pipelines using probabilistic tractography methods. Our results highlight the need for further advances tractography and streamline filtering to improve the accuracy of connectome mapping.

Connectomic Networks and Their Impact on Clinical Outcomes in Glioma Treatment: A Review

AbstractThe emerging field of connectomics has provided an improved understanding of the structural and functional organization of the human brain into large-scale brain networks. Recent studies have helped define the canonical neurological networks and outline how considering their presence may aid in surgical decision-making in brain tumor patients. Gliomas represent one of the most common types of brain tumor and often involve displacement and/or infiltration of neurological pathways, suggesting an opportunity to use connectomic maps to improve patient morbidity and mortality based on oncofunctional goals. This review aims to provide a working knowledge of important neurological networks, examine the use of networks in surgical planning, and describe the current literature discussing the impact of these networks on clinical outcomes in glioma resection.

Hierarchical fluctuation shapes a dynamic flow linked to states of consciousness

Consciousness arises from the spatiotemporal neural dynamics, however, its relationship with neural flexibility and regional specialization remains elusive. We identified a consciousness-related signature marked by shifting spontaneous fluctuations along a unimodal-transmodal cortical axis. This simple signature is sensitive to altered states of consciousness in single individuals, exhibiting abnormal elevation under psychedelics and in psychosis. The hierarchical dynamic reflects brain state changes in global integration and connectome diversity under task-free conditions. Quasi-periodic pattern detection revealed that hierarchical heterogeneity as spatiotemporally propagating waves linking to arousal. A similar pattern can be observed in macaque electrocorticography. Furthermore, the spatial distribution of principal cortical gradient preferentially recapitulated the genetic transcription levels of the histaminergic system and that of the functional connectome mapping of the tuberomammillary nucleus, which promotes wakefulness. Combining behavioral, neuroimaging, electrophysiological, and transcriptomic evidence, we propose that global consciousness is supported by efficient hierarchical processing constrained along a low-dimensional macroscale gradient.

Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

The prefrontal cortex (PFC) has dramatically expanded in primates, but its organization and interactions with other brain regions are only partially understood. We performed high-resolution connectomic mapping of the marmoset PFC and found two contrasting corticocortical and corticostriatal projection patterns: "patchy" projections that formed many columns of submillimeter scale in nearby and distant regions and "diffuse" projections that spread widely across the cortex and striatum. Parcellation-free analyses revealed representations of PFC gradients in these projections' local and global distribution patterns. We also demonstrated column-scale precision of reciprocal corticocortical connectivity, suggesting that PFC contains a mosaic of discrete columns. Diffuse projections showed considerable diversity in the laminar patterns of axonal spread. Altogether, these fine-grained analyses reveal important principles of local and long-distance PFC circuits in marmosets and provide insights into the functional organization of the primate brain.

A framework for focal and connectomic mapping of transiently disrupted brain function

The distributed nature of the neural substrate, and the difficulty of establishing necessity from correlative data, combine to render the mapping of brain function a far harder task than it seems. Methods capable of combining connective anatomical information with focal disruption of function are needed to disambiguate local from global neural dependence, and critical from merely coincidental activity. Here we present a comprehensive framework for focal and connective spatial inference based on sparse disruptive data, and demonstrate its application in the context of transient direct electrical stimulation of the human medial frontal wall during the pre-surgical evaluation of patients with focal epilepsy. Our framework formalizes voxel-wise mass-univariate inference on sparsely sampled data within the statistical parametric mapping framework, encompassing the analysis of distributed maps defined by any criterion of connectivity. Applied to the medial frontal wall, this transient dysconnectome approach reveals marked discrepancies between local and distributed associations of major categories of motor and sensory behaviour, revealing differentiation by remote connectivity to which purely local analysis is blind. Our framework enables disruptive mapping of the human brain based on sparsely sampled data with minimal spatial assumptions, good statistical efficiency, flexible model formulation, and explicit comparison of local and distributed effects.

Structural and functional connectivity reconstruction with CATO - A Connectivity Analysis TOolbox

We describe a Connectivity Analysis TOolbox (CATO) for the reconstruction of structural and functional brain connectivity based on diffusion weighted imaging and resting-state functional MRI data. CATO is a multimodal software package that enables researchers to run end-to-end reconstructions from MRI data to structural and functional connectome maps, customize their analyses and utilize various software packages to preprocess data. Structural and functional connectome maps can be reconstructed with respect to user-defined (sub)cortical atlases providing aligned connectivity matrices for integrative multimodal analyses. We outline the implementation and usage of the structural and functional processing pipelines in CATO. Performance was calibrated with respect to simulated diffusion weighted imaging data from the ITC2015 challenge and test-retest diffusion weighted imaging data and resting-state functional MRI data from the Human Connectome Project. CATO is open-source software distributed under the MIT License and available as a MATLAB toolbox and as a stand-alone application at www.dutchconnectomelab.nl/CATO.

Virtual Fly Brain-An interactive atlas of the Drosophila nervous system.

As a model organism, Drosophila is uniquely placed to contribute to our understanding of how brains control complex behavior. Not only does it have complex adaptive behaviors, but also a uniquely powerful genetic toolkit, increasingly complete dense connectomic maps of the central nervous system and a rapidly growing set of transcriptomic profiles of cell types. But this also poses a challenge: Given the massive amounts of available data, how are researchers to Find, Access, Integrate and Reuse (FAIR) relevant data in order to develop an integrated anatomical and molecular picture of circuits, inform hypothesis generation, and find reagents for experiments to test these hypotheses? The Virtual Fly Brain (virtualflybrain.org) web application & API provide a solution to this problem, using FAIR principles to integrate 3D images of neurons and brain regions, connectomics, transcriptomics and reagent expression data covering the whole CNS in both larva and adult. Users can search for neurons, neuroanatomy and reagents by name, location, or connectivity, via text search, clicking on 3D images, search-by-image, and queries by type (e.g., dopaminergic neuron) or properties (e.g., synaptic input in the antennal lobe). Returned results include cross-registered 3D images that can be explored in linked 2D and 3D browsers or downloaded under open licenses, and extensive descriptions of cell types and regions curated from the literature. These solutions are potentially extensible to cover similar atlasing and data integration challenges in vertebrates.

Graph Theory Measures and Their Application to Neurosurgical Eloquence.

Improving patient safety and preserving eloquent brain are crucial in neurosurgery. Since there is significant clinical variability in post-operative lesions suffered by patients who undergo surgery in the same areas deemed compensable, there is an unknown degree of inter-individual variability in brain 'eloquence'. Advances in connectomic mapping efforts through diffusion tractography allow for utilization of non-invasive imaging and statistical modeling to graphically represent the brain. Extending the definition of brain eloquence to graph theory measures of hubness and centrality may help to improve our understanding of individual variability in brain eloquence and lesion responses. While functional deficits cannot be immediately determined intra-operatively, there has been potential shown by emerging technologies in mapping of hub nodes as an add-on to existing surgical navigation modalities to improve individual surgical outcomes. This review aims to outline and review current research surrounding novel graph theoretical concepts of hubness, centrality, and eloquence and specifically its relevance to brain mapping for pre-operative planning and intra-operative navigation in neurosurgery.

Large‐Scale Network Dysfunction in Dementia with Lewy Bodies: Preliminary Results from an fMRI Connectomic Mapping Study

AbstractBackgroundThe diagnosis of dementia with Lewy bodies (DLB) is often delayed in clinical practice. The sensitivity and specificity of structural MRI is suboptimal: a multisite study with autopsy confirmation demonstrated 64% sensitivity and 68% specificity for differentiating DLB from Alzheimer's Disease (AD; Harper et.al, 2016). There is an urgent need to develop additional reliable biomarkers for DLB. We describe resting state functional MRI (rsfMRI) results using an automated connectome mapping program (Infinitome).MethodParticipants meeting criteria for probable DLB (McKeith et al, 2017) aged between 40 ‐90 years with a MMSE &gt;15 were recruited from a multidisciplinary dementia clinic in this cross‐sectional study. MRI imaging was performed using a 3T Siemens scanner. DTI (diffusion tensor imaging), rsfMRI and structural images were gathered and analyzed through Infinitome (Rosenbloom et al, 2021), a program that creates a machine learning‐based, subject‐specific version of the Human Connectome Project‐Multimodal Parcellation atlas based upon diffusion tractography structural connectivity.ResultTwenty‐six participants were contacted, of which 14 (54%) were consented and one withdrawn by the investigator. Of the 13 subjects that completed the study, 77% were male, 100% white and non‐Hispanic origin, with mean age 73.29 years (± 5.8), and average MMSE score 23.14 (±4.3). All participants demonstrated abnormal connectivity in regions involving visuospatial attention (areas 8Av, PGs, TE2a) and language processing (areas 55b, TGd, TGv; Table 1; Baker et al, 2018). Five parcellations were part of the extended default mode network (DMN) whereas one was part of the extended central executive network. Seven participants demonstrated changes in connectivity of area 46 (R &amp; L; cognitive processing and mood) within the salience network (SN).ConclusionPreliminary findings suggest reduced connectivity in regions involved in visuospatial attention, language processing, and mood within in large‐scale networks such as the DMN and SN, consistent with previously published fMRI studies in DLB (Nicastro 2021; Schumacher 2018). The use of rsfMRI and connectome mapping may enable identification of a distinct radiological “signature” for DLB. Future research will evaluate rsfMRI features that distinguish DLB from AD.

Resting-state Functional Connectivity During Controlled Respiratory Cycles Using Functional Magnetic Resonance Imaging.

This study aimed to assess the effect of controlled mouth breathing during the resting state using functional magnetic resonance imaging (fMRI). Eleven subjects participated in this experiment in which the controlled "Nose" and "Mouth" breathings of 6 s respiratory cycle were performed with a visual cue at 3T MRI. Voxel-wise seed-to-voxel maps and whole-brain region of interest (ROI)-to-ROI connectome maps were analyzed in both "Nose>Mouth" and "Mouth>Nose" contrasts. As a result, there were more connection pairs in the "Mouth" breathing condition, i.e., 14 seeds and 14 connecting pairs in the "Mouth>Nose" contrast, compared to 7 seeds and 4 connecting pairs in the "Nose>Mouth" contrast (false discovery rate [FDR] of P<0.05). The present study demonstrated that mouth breathing with controlled respiratory cycles could significantly induce alterations in functional connectivity in the resting-state network, suggesting that it can differently affect resting brain function; in particular, the brain can hardly rest during mouth breathing, as opposed to conventional nasal breathing.

Fingerprinting seizure outcome after temporal lobe surgery using preoperative connectomic mapping.

This scientific commentary refers to 'Presurgical temporal lobe epilepsy connectome fingerprint for seizure outcome prediction' by Morgan et al. (https://doi.org/10.1093/braincomms/fcac128) in Brain Communications.

Insect neuroscience: Filling the knowledge gap on gap junctions

Gap junctions, too small to spot in images used to create connectome maps, play outsized roles in shaping neural activity. A recent study reveals a surprising new gap junction function: they can stabilize a neuron's membrane potential against unwanted oscillations.