publications
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2024
- Nat. NeurosciVentral attention network connectivity is linked to cortical maturation and cognitive ability in childhoodHao-Ming Dong, Xi-Han Zhang , Loic Labache, Shaoshi Zhang , Leon Qi Rong Ooi , BT Thomas Yeo, Avram J Holmes, Daniel S Margulies , and Xi-Nian ZuoNature Neuroscience, 2024
The human brain experiences functional changes through childhood and adolescence, shifting from an organizational framework anchored within sensorimotor and visual regions into one that is balanced through interactions with later-maturing aspects of association cortex. Here, we link this profile of functional reorganization to the development of ventral attention network connectivity across independent datasets. We demonstrate that maturational changes in cortical organization link preferentially to within-network connectivity and heightened degree centrality in the ventral attention network, whereas connectivity within network-linked vertices predicts cognitive ability. This connectivity is associated closely with maturational refinement of cortical organization. Children with low ventral attention network connectivity exhibit adolescent-like topographical profiles, suggesting that attentional systems may be relevant in understanding how brain functions are refined across development. These data suggest a role for attention networks in supporting age-dependent shifts in cortical organization and cognition across childhood and adolescence.
- Commun. BiolA shared spatial topography links the functional connectome correlates of cocaine use disorder and dopamine D2/3 receptor densitiesJocelyn A Ricard , Loic Labache, Ashlea Segal , Elvisha Dhamala , Carrisa V Cocuzza , Grant Jones , Sarah W Yip , Sidhant Chopra, and Avram J HolmesCommunications Biology, 2024
The biological mechanisms that contribute to cocaine and other substance use disorders involve an array of cortical and subcortical systems. Prior work on the development and maintenance of substance use has largely focused on cortico-striatal circuits, with relatively less attention on alterations within and across large-scale functional brain networks, and associated aspects of the dopamine system. Here, we characterize patterns of functional connectivity in cocaine use disorder and their spatial association with neurotransmitter receptor densities and transporter bindings assessed through PET. Profiles of functional connectivity in cocaine use disorder reliably linked with spatial densities of dopamine D2/3 receptors across independent datasets. These findings demonstrate that the topography of dopamine receptor densities may underlie patterns of functional connectivity in cocaine use disorder, as assessed through fMRI.
- Imaging NeuroscienceAtlas for the Lateralized Visuospatial Attention Networks (ALANs): Insights from fMRI and Network AnalysesImaging Neuroscience, 2024
Hemispheric specialization is central to human evolution and fundamental to human cognitive abilities. While being a defining feature of functional brain architecture, hemispheric specialization is overlooked to derive brain parcellations. Alongside language, which is typically lateralized in the left hemisphere, visuospatial attention is set to be its counterpart in the opposite hemisphere. However, it remains uncertain to what extent the anatomical and functional underpinnings of lateralized visuospatial attention mirror those supporting language. Building on our previous work, which established a lateralized brain atlas for language, we propose a comprehensive cerebral lateralized atlas delineating the anatomo-functional bases of visuospatial attention, Atlas for Lateralized visuospatial Attentional Networks (ALANs). Combining task and resting-state functional connectivity analyses, we identified 95 lateralized brain areas comprising three networks supporting visual (visu), motor (somato-motor), and spatial processing (posterior-medial) processes at work during a line judgment bisection task, and two large-scale networks related to integrated visuospatial attention processes, the parieto-frontal and temporo-frontal networks. We identify hubs playing a pivotal role in the intra-hemispheric interaction within visuospatial attentional networks. The rightward lateralized parieto-frontal encompasses one hub, the inferior frontal sulcus, while the temporo-frontal network encompasses two right hubs: the inferior frontal cortex (pars triangularis and the anterior insula) and the posterior part of the superior temporal sulcus. Compared with our language lateralized atlas, we demonstrated that specific regions within these networks encompass the homotope of the language network from the left hemisphere. This atlas of visuospatial attention provides valuable insights for future investigations into the variability of visuospatial attention and hemispheric specialization research. Additionally, it facilitates more effective comparisons among different studies, thereby enhancing the robustness and reliability of research in the field of attention.
- medRxivThe Transdiagnostic Connectome Project: a richly phenotyped open dataset for advancing the study of brain-behavior relationships in psychiatrySidhant Chopra, Carrisa V. Cocuzza , Connor Lawhead , Jocelyn A. Ricard , Loic Labache, Lauren M. Patrick , Poornima Kumar , Arielle Rubenstein , Julia Moses , Lia Chen , Crystal Blankenbaker , Bryce Gillis , Laura T. Germine , Ilan Harpaz-Rote , BT Thomas Yeo, Justin T. Baker , and Avram J. HolmesmedRxiv, 2024
An important aim in psychiatry is the establishment of valid and reliable associations linking profiles of brain functioning to clinically relevant symptoms and behaviors across patient populations. To advance progress in this area, we introduce an open dataset containing behavioral and neuroimaging data from 241 individuals aged 18 to 70, comprising 148 individuals meeting diagnostic criteria for a broad range of psychiatric illnesses and a healthy comparison group of 93 individuals. These data include high-resolution anatomical scans, multiple resting-state, and task-based functional MRI runs. Additionally, participants completed over 50 psychological and cognitive assessments. Here, we detail available behavioral data as well as raw and processed MRI derivatives. Associations between data processing and quality metrics, such as head motion, are reported. Processed data exhibit classic task activation effects and canonical functional network organization. Overall, we provide a comprehensive and analysis-ready transdiagnostic dataset, which we hope will accelerate the identification of illness-relevant features of brain functioning, enabling future discoveries in basic and clinical neuroscience.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThis work was supported by the National Institute of Mental Health (R01MH123245 to AJH and R01MH120080 to AJH and BTTY). BTTY is also supported by the NUS Yong Loo Lin School of Medicine (NUHSRO/2020/124/TMR/LOA), the Singapore National Medical Research Council (NMRC) LCG (OFLCG19May-0035), NMRC CTG-IIT (CTGIIT23jan-0001), NMRC STaR (STaR20nov-0003), Singapore Ministry of Health (MOH) Centre Grant (CG21APR1009), the Temasek Foundation (TF2223-IMH-01), and the United States National Institutes of Health (R01MH120080). Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not reflect the views of the grantors. SC is supported by an American Australian Association Graduate Education Fund Scholarship. JAR is supported by the Stanford University Knight-Hennessy Scholars Program, and the National Academies of Sciences, Engineering, and Medicines Ford Foundation Predoctoral Fellowship. LMP is supported by a T32 Fellowship from the National Institute of Mental Health (T32MH019112-32).Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:IRB of both Yale University and McLean Hospital (Partners Healthcare) gave ethical approval for this work. Representative study consent forms from each site are provided in Supplementary Appendix A.I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesRaw neuroimaging data and all behavioral measures can be accessed via OpenNeuro (https://openneuro.org/datasets/ds005237). Raw and processed neuroimaging data, as well as all behavioral measures, can be openly accessed via the NDA (https://nda.nih.gov/edit_collection.html?id=3552) upon publication. https://openneuro.org/datasets/ds005237
2023
- Aperture NeuroA Practical Guide for Generating Reproducible and Programmatic Neuroimaging VisualizationsSidhant Chopra, Loic Labache, Elvisha Dhamala , Edwina R Orchard , and Avram J HolmesAperture Neuro, 2023
Neuroimaging visualizations form the centerpiece of the interpretation and communication of scientific results, and are a cornerstone for data quality control. Often, these images and figures are produced by manually changing settings on Graphical User Interfaces (GUIs). There now exist many well-documented code-based brain visualization tools that allow users to use code to programmatically generate publication-ready figures directly within programming environments such as R, Python and MATLAB. Here, we provide a rationale for the wide-spread adoption of code-generated brain visualizations by highlighting corresponding advantages in replicability, flexibility, and integration over GUI based tools. We then provide a practical guide outlining the steps required to generate these code-based brain visualizations. We also present a comprehensive table of tools currently available for programmatic brain visualizations and provide examples of visualizations and associated code as a point of reference (https://sidchop.shinyapps.io/braincode_selector/). Finally, we provide a web-app that generates simple code-templates as starting points for these visualizations (https://sidchop.shinyapps.io/braincode/).
- Nat. CommunLanguage network lateralization is reflected throughout the macroscale functional organization of cortexNature Communications, 2023
Hemispheric specialization is a fundamental feature of human brain organization. However, it is not yet clear to what extent the lateralization of specific cognitive processes may be evident throughout the broad functional architecture of cortex. While the majority of people exhibit left-hemispheric language dominance, a substantial minority of the population shows reverse lateralization. Using twin and family data from the Human Connectome Project, we provide evidence that atypical language dominance is associated with global shifts in cortical organization. Individuals with atypical language organization exhibit corresponding hemispheric differences in the macroscale functional gradients that situate discrete large-scale networks along a continuous spectrum, extending from unimodal through association territories. Analyses reveal that both language lateralization and gradient asymmetries are, in part, driven by genetic factors. These findings pave the way for a deeper understanding of the origins and relationships linking population-level variability in hemispheric specialization and global properties of cortical organization.
- bioRxivWhen Age Tips the Balance: a Dual Mechanism Affecting Hemispheric Specialization for LanguagebioRxiv, 2023
Aging engenders neuroadaptations, generally reducing specificity and selectivity in functional brain responses. Our investigation delves into the functional specialization of brain hemispheres within language-related networks across adulthood. In a cohort of 728 healthy adults spanning ages 18 to 88, we modeled the trajectories of inter-hemispheric asymmetry concerning the principal functional gradient across 37 homotopic regions of interest (hROIs) of an extensive language network known as the Language-and-Memory Network. Our findings reveal that over two-thirds of Language-and-Memory Network hROIs undergo asymmetry changes with age, falling into two main clusters. The first cluster evolves from left-sided specialization to right-sided tendencies, while the second cluster transitions from right-sided asymmetry to left-hemisphere dominance. These reversed asymmetry shifts manifest around midlife, occurring after age 50, and are associated with poorer language production performance. Our results provide valuable insights into the influence of functional brain asymmetries on language proficiency and present a dynamic perspective on brain plasticity during the typical aging process.
2022
- Brain Struct. Funct.Stroke disconnectome decodes reading networksStephanie J Forkel, Loic Labache, Parashkev Nachev , Michel Schotten , and Isabelle HeslingBrain Structure and Function, 2022
Cognitive functional neuroimaging has been around for over 30 years and has shed light on the brain areas relevant for reading. However, new methodological developments enable mapping the interaction between functional imaging and the underlying white matter networks. In this study, we used such a novel method, called the disconnectome, to decode the reading circuitry in the brain. We used the resulting disconnection patterns to predict a typical lesion that would lead to reading deficits after brain damage. Our results suggest that white matter connections critical for reading include fronto-parietal U-shaped fibres and the vertical occipital fasciculus (VOF). The lesion most predictive of a reading deficit would impinge on the left temporal, occipital, and inferior parietal gyri. This novel framework can systematically be applied to bridge the gap between the neuropathology of language and cognitive neuroscience.
2021
- Cereb. CortexAtlas55+: brain functional atlas of resting-state networks for late adulthoodGaelle E Doucet, Loic Labache, Paul M Thompson , Marc Joliot, Sophia Frangou , and Alzheimer’s Disease Neuroimaging InitiativeCerebral Cortex, 2021
Currently, several human brain functional atlases are used to define the spatial constituents of the resting-state networks (RSNs). However, the only brain atlases available are derived from samples of young adults. As brain networks are continuously reconfigured throughout life, the lack of brain atlases derived from older populations may influence RSN results in late adulthood. To address this gap, the aim of the study was to construct a reliable brain atlas derived only from older participants. We leveraged resting-state functional magnetic resonance imaging data from three cohorts of healthy older adults (total N = 563; age = 55–95 years) and a younger-adult cohort (N = 128; age = 18–35 years). We identified the major RSNs and their subdivisions across all older-adult cohorts. We demonstrated high spatial reproducibility of these RSNs with an average spatial overlap of 67%. Importantly, the RSNs derived from the older-adult cohorts were spatially different from those derived from the younger-adult cohort (P = 2.3 × 10−3). Lastly, we constructed a novel brain atlas, called Atlas55+, which includes the consensus of the major RSNs and their subdivisions across the older-adult cohorts. Thus, Atlas55+ provides a reliable age-appropriate template for RSNs in late adulthood and is publicly available. Our results confirm the need for age-appropriate functional atlases for studies investigating aging-related brain mechanisms.
- LateralityNeural support of manual preference revealed by BOLD variations during right and left finger-tapping in a sample of 287 healthy adults balanced for handednessLaterality, 2021
We have identified the brain areas involved in Manual Preference (MP) in 143 left-handers (LH) and 144 right-handers (RH). First, we selected the pairs of homotopic regions of interest (hROIs) of the AICHA atlas with significant contralateral activation and asymmetry during the right hand and the left hand Finger-Tapping (FT) both in RH and LH. Thirteen hROIs were selected, including the primary and secondary sensorimotor and premotor cortices, thalamus, dorsal putamen, and cerebellar lobule IV. In both groups, contralateral activations and ipsilateral deactivations were seen, with stronger asymmetries when the preferred hand was used. Comparing with different models for the prediction of MP, we found that the differences in activity during preferred hand minus non-preferred hand movement in 11 contralateral and/or ipsilateral hROIS were best at explaining handedness distribution. Two different mechanisms were identified: 1. Stronger contralateral activity of cortical and cerebellar motor areas during right hand movement, seen in both groups but modulated by handedness; 2. Stronger deactivation in ipsilateral areas during dominant hand movement in both groups, LH here mirroring RH. The present study thus demonstrates that handedness neural support is complex and not simply based on a mirrored organization of hand motor areas.
2020
- eLifeTypical and atypical language brain organization based on intrinsic connectivity and multitask functional asymmetriesLoic Labache, Bernard Mazoyer, Marc Joliot, Fabrice Crivello , Isabelle Hesling, and Nathalie Tzourio-MazoyerElife, 2020
Based on the joint investigation in 287 healthy volunteers (150 left-Handers (LH)) of language task-induced asymmetries and intrinsic connectivity strength of the sentence-processing supramodal network, we show that individuals with atypical rightward language lateralization (N = 30, 25 LH) do not rely on an organization that simply mirrors that of typical leftward lateralized individuals. Actually, the resting-state organization in the atypicals showed that their sentence processing was underpinned by left and right networks both wired for language processing and highly interacting by strong interhemispheric intrinsic connectivity and larger corpus callosum volume. Such a loose hemispheric specialization for language permits the hosting of language in either the left and/or right hemisphere as assessed by a very high incidence of dissociations across various language task-induced asymmetries in this group.
- arXivStudy of inter-individual variability of three-dimensional data table: detection of unstable variables and samplesLoic Labache, Marc Joliot, Gaelle E Doucet, and Jérôme SaraccoarXiv preprint arXiv:2004.05033, 2020
We propose two methodologies in order to better understand the inter-individual variability of resting-state functional Magnetic Resonance Imaging (fMRI) brain data. The aim of the study was to quantify whether the average dendrogram is representative of the initial population and to identify its possible sources of instability. The average dendrogram is based on the Pearson correlation between resting-state networks. The first method identifies networks that can lead to unstable partitions of the average dendrogram. The second method identified homogeneous sub-samples of participants for whom their associated average dendrograms were more stable than that of the whole sample. The two suggested methods have shown significant quantifiable behavioral data results with regards to detecting an unstable network or presence of subpopulations when the noise level does not conceal the structure of the data. These two methods have been successfully applied to establish a cerebral atlas for late adulthood. The first method made it clear that there was no unstable network among the atlas networks. The second method highlighted the presence of two distinct sub-populations with different age-related brain organizations.
2019
- Brain Struct. Funct.A SENtence Supramodal Areas AtlaS (SENSAAS) based on multiple task-induced activation mapping and graph analysis of intrinsic connectivity in 144 healthy right-handersLoic Labache, Marc Joliot, Jérôme Saracco , Gaël Jobard , Isabelle Hesling, Laure Zago, Emmanuel Mellet , Laurent Petit, Fabrice Crivello , Bernard Mazoyer, and othersBrain Structure and Function, 2019
We herein propose an atlas of 32 sentence-related areas based on a 3-step method combining the analysis of activation and asymmetry during multiple language tasks with hierarchical clustering of resting-state connectivity and graph analyses. 144 healthy right-handers performed fMRI runs based on language production, reading and listening, both with sentences and lists of over-learned words. Sentence minus word-list BOLD contrast and left-minus-right BOLD asymmetry for each task were computed in pairs of homotopic regions of interest (hROIs) from the AICHA atlas. Thirty-two hROIs were identified that were conjointly activated and leftward asymmetrical in each of the three language contrasts. Analysis of resting-state temporal correlations of BOLD variations between these 32 hROIs allowed the segregation of a core network, SENT_CORE including 18 hROIs. Resting-state graph analysis applied to SENT_CORE hROIs revealed that the pars triangularis of the inferior frontal gyrus and the superior temporal sulcus were hubs based on their degree centrality (DC), betweenness, and participation values corresponding to epicentres of sentence processing. Positive correlations between DC and BOLD activation values for SENT_CORE hROIs were observed across individuals and across regions regardless of the task: the more a SENT_CORE area is connected at rest the stronger it is activated during sentence processing. DC measurements in SENT_CORE may thus be a valuable index for the evaluation of inter-individual variations in language areas functional activity in relation to anatomical or clinical patterns in large populations.
- Brain Struct. Funct.Large-scale plurimodal networks common to listening to, producing and reading word lists: an fMRI study combining task-induced activation and intrinsic connectivity in 144 right-handersBrain Structure and Function, 2019
We aimed at identifying plurimodal large-scale networks for producing, listening to and reading word lists based on the combined analyses of task-induced activation and resting-state intrinsic connectivity in 144 healthy right-handers. In the first step, we identified the regions in each hemisphere showing joint activation and joint asymmetry during the three tasks. In the left hemisphere, 14 homotopic regions of interest (hROIs) located in the left Rolandic sulcus, precentral gyrus, cingulate gyrus, cuneus and inferior supramarginal gyrus (SMG) met this criterion, and 7 hROIs located in the right hemisphere were located in the preSMA, medial superior frontal gyrus, precuneus and superior temporal sulcus (STS). In a second step, we calculated the BOLD temporal correlations across these 21 hROIs at rest and conducted a hierarchical clustering analysis to unravel their network organization. Two networks were identified, including the WORD-LIST_CORE network that aggregated 14 motor, premotor and phonemic areas in the left hemisphere plus the right STS that corresponded to the posterior human voice area (pHVA). The present results revealed that word-list processing is based on left articulatory and storage areas supporting the action–perception cycle common not only to production and listening but also to reading. The inclusion of the right pHVA acting as a prosodic integrative area highlights the importance of prosody in the three modalities and reveals an intertwining across hemispheres between prosodic (pHVA) and phonemic (left SMG) processing. These results are consistent with the motor theory of speech postulating that articulatory gestures are the central motor units on which word perception, production, and reading develop and act together.
