Conn: a functional connectivity toolbox for correlated and anticorrelated brain networks.
paper
Cited
Public
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- Authors
- Whitfield-Gabrieli, Susan; Nieto-Castanon, Alfonso
- Year
- 2012
- Journal
- Brain connectivity
- PMID
- 22642651
- DOI
- 10.1089/brain.2012.0073
Resting state functional connectivity reveals intrinsic, spontaneous networks that elucidate the functional architecture of the human brain. However, valid statistical analysis used to identify such networks must address sources of noise in order to avoid possible confounds such as spurious correlations based on non-neuronal sources. We have developed a functional connectivity toolbox Conn ( www.nitrc.org/projects/conn ) that implements the component-based noise correction method (CompCor) strategy for physiological and other noise source reduction, additional removal of movement, and temporal covariates, temporal filtering and windowing of the residual blood oxygen level-dependent (BOLD) contrast signal, first-level estimation of multiple standard functional connectivity magnetic resonance imaging (fcMRI) measures, and second-level random-effect analysis for resting state as well as task-related data. Compared to methods that rely on global signal regression, the CompCor noise reduction method allows for interpretation of anticorrelations as there is no regression of the global signal. The toolbox implements fcMRI measures, such as estimation of seed-to-voxel and region of interest (ROI)-to-ROI functional correlations, as well as semipartial correlation and bivariate/multivariate regression analysis for multiple ROI sources, graph theoretical analysis, and novel voxel-to-voxel analysis of functional connectivity. We describe the methods implemented in the Conn toolbox for the analysis of fcMRI data, together with examples of use and interscan reliability estimates of all the implemented fcMRI measures. The results indicate that the CompCor method increases the sensitivity and selectivity of fcMRI analysis, and show a high degree of interscan reliability for many fcMRI measures.
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| Ultrasound Neuromodulation With Transcranial Pulse Stimulation in Alzheimer Disease: A Randomized Clinical Trial. | Matt E et al. | β | 2025 | β |
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| Unraveling trauma memory: Differential functional connectivity profiles of anterior and posterior hippocampus in post-traumatic stress disorder and its dissociative subtype. | Chaposhloo M et al. | β | 2025 | β |
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| VOXEL-TO-BLADDER FULLNESS SENSATION. | Bayer A et al. | β | 2025 | β |
| Voxel-Wise or Region-Wise Nuisance Regression for Functional Connectivity Analyses: Does It Matter? | Muganga T et al. | β | 2025 | β |
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| Younger adult brain utilizes interhemispheric strategy via ipsilateral dorsal premotor cortex for fine control of dexterous finger movements, unlike the aging brain. | Miura G et al. | β | 2025 | β |
| A Bayesian Multiplex Graph Classifier of Functional Brain Connectivity Across Diverse Tasks of Cognitive Control. | Guha S et al. | β | 2024 | β |
| Aberrant Functional Connectivity of the Salience Network in Adult Patients with Tic Disorders: A Resting-State fMRI Study. | Orth L et al. | β | 2024 | β |
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| Brain alterations in individuals with exercise dependence: A multimodal neuroimaging investigation. | Schaub AC et al. | β | 2024 | β |
| Brain-based graph-theoretical predictive modeling to map the trajectory of anhedonia, impulsivity, and hypomania from the human functional connectome. | Dan R et al. | β | 2024 | β |
| Brain Connectomics Improve the Prediction of High-Risk Depression Profiles in the First Year following Breast Cancer Diagnosis. | Liang MZ et al. | β | 2024 | β |
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| Cerebral Mechanism of Tuina on the Descending Pain Inhibitory System in Knee Osteoarthritis: Protocol for a Randomized Controlled Trial. | Xu H et al. | β | 2024 | β |
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| Concurrent optoacoustic tomography and magnetic resonance imaging of resting-state functional connectivity in the mouse brain. | Gezginer I et al. | β | 2024 | β |
| Connectivity Changes Following Episodic Future Thinking in Alcohol Use Disorder. | Myslowski J et al. | β | 2024 | β |
| Connectivity, Pathology, and ApoE4 Interactions Predict Longitudinal Tau Spatial Progression and Memory. | Ziontz J et al. | β | 2024 | β |
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| Data-Driven Discovery of Movement-Linked Heterogeneity in Neurodegenerative Diseases. | Endo M et al. | β | 2024 | β |
| Decline in Sensory Integration in Old Age and Its Related Functional Brain Connectivity Correlates Observed during a Virtual Reality Task. | Inagaki S et al. | β | 2024 | β |
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| Delayed Recovery After Exercise-Induced Pain in People with Chronic Widespread Muscle Pain Related to Cortical Connectivity. | Bishop MD et al. | β | 2024 | β |
| Depressed patients with childhood maltreatment display altered intra- and inter-network resting state functional connectivity. | GΓ‘lber M et al. | β | 2024 | β |
| Detecting Alzheimer's Disease Stages and Frontotemporal Dementia in Time Courses of Resting-State fMRI Data Using a Machine Learning Approach. | Sadeghi MA et al. | β | 2024 | β |
| Differences in brain connectivity between older adults practicing Tai Chi and Water Aerobics: a case-control study. | Port AP et al. | β | 2024 | β |
| Differences in Grey Matter Concentrations and Functional Connectivity between Young Carriers and Non-Carriers of the APOE Ξ΅4 Genotype. | MuΓ±oz-Neira C et al. | β | 2024 | β |
| Differences in Static and Dynamic Resting-State Functional Connectivity between Migraineurs with and without Photophobia, without Phonophobia or Osmophobia. | Imai N et al. | β | 2024 | β |
| Differential neural correlates underlying visuospatial versus semantic reasoning in autistic children. | DegrΓ©-Pelletier J et al. | β | 2024 | β |
| Differential patterns of functional connectivity in tremor dominant Parkinson's disease and essential tremor plus. | Prasad S et al. | β | 2024 | β |
| Directed functional connectivity of the default-mode-network of young and older healthy subjects. | Goelman G et al. | β | 2024 | β |
| Dissociable Contributions of the Medial Parietal Cortex to Recognition Memory. | Koslov SR et al. | β | 2024 | β |
| Distinct connectivity patterns in bipolar and unipolar depression: a functional connectivity multivariate pattern analysis study. | Pastrnak M et al. | β | 2024 | β |
| Distinctive and Complementary Roles of Default Mode Network Subsystems in Semantic Cognition. | Shao X et al. | β | 2024 | β |
| Distinct neural signatures of pulvinar in C9orf72 amyotrophic lateral sclerosis mutation carriers and noncarriers. | Nigri A et al. | β | 2024 | β |
| Distinct resting-state functional connectivity of the anterior cingulate cortex subregions in first-episode schizophrenia. | Huang H et al. | β | 2024 | β |
| DPABINet: A toolbox for brain network and graph theoretical analyses. | Yan CG et al. | β | 2024 | β |
| Dynamic Functional Connectivity Correlates of Trait Mindfulness in Early Adolescence. | Treves IN et al. | β | 2024 | β |
| Dynamic functional connectivity in the right temporoparietal junction captures variations in male autistic trait expression. | Bravo Balsa L et al. | β | 2024 | β |
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| Effects of acupuncture at the Taichong (LIV3) and Hegu (LI4) points on functional connectivity with the retrosplenial cortex in patients with Alzheimer's disease. | Wang J et al. | β | 2024 | β |
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| Evaluating the Effect of Alzheimer's Disease-Related Biomarker Change in Corticobasal Syndrome and Progressive Supranuclear Palsy. | Garcia-Cordero I et al. | β | 2024 | β |
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| Frontal Pole Neuromodulation for Impulsivity and Suicidality in Veterans With Mild Traumatic Brain Injury and Common Co-Occurring Mental Health Conditions: Protocol for a Pilot Randomized Controlled Trial. | Bernanke A et al. | β | 2024 | β |
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| Frontoparietal network topology as a neural marker of musical perceptual abilities. | Lumaca M et al. | β | 2024 | β |
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| Functional Brain Network Alterations Against Scaling. | Eldaly ABM et al. | β | 2024 | β |
| Functional Brain Network of Trait Impulsivity: Whole-Brain Functional Connectivity Predicts Self-Reported Impulsivity. | HΓΌpen P et al. | β | 2024 | β |
| Functional connectivity associated with attention networks differs among subgroups of fibromyalgia patients: an observational case-control study. | Aoe T et al. | β | 2024 | β |
| Functional Connectivity Biomarker Extraction for Schizophrenia Based on Energy Landscape Machine Learning Techniques. | Allen JD et al. | β | 2024 | β |
| Functional connectivity changes in neurodegenerative biomarker-positive athletes with repeated concussions. | Garcia-Cordero I et al. | β | 2024 | β |
| Functional connectivity compensation in Parkinson's disease with freezing of gait. | Huang LC et al. | β | 2024 | β |
| Functional connectivity during facial and vocal emotion recognition: Preliminary evidence for dissociations in developmental change by nonverbal modality. | Morningstar M et al. | β | 2024 | β |
| Functional connectivity in autism spectrum disorder evaluated using rs-fMRI and DKI. | Nagai Y et al. | β | 2024 | β |
| Functional connectivity in complex regional pain syndrome: A bicentric study. | Hok P et al. | β | 2024 | β |
| Functional PET/MRI reveals active inhibition of neuronal activity during optogenetic activation of the nigrostriatal pathway. | Haas S et al. | β | 2024 | β |
| Genetic fingerprinting with heritable phenotypes of the resting-state brain network topology. | Pourmotabbed H et al. | β | 2024 | β |
| Global changes in the pattern of connectivity in developmental prosopagnosia. | Epihova G et al. | β | 2024 | β |
| Graph analysis uncovers an opposing impact of methylphenidate on connectivity patterns within default mode network sub-divisions. | Daood M et al. | β | 2024 | β |
| Health literacy, but not memory, is associated with hippocampal connectivity in adults with low levels of formal education. | de Paula FranΓ§a Resende E et al. | β | 2024 | β |
| Higher-order functional brain networks and anterior cingulate glutamate + glutamine (Glx) in antipsychotic-naΓ―ve first episode psychosis patients. | Maximo JO et al. | β | 2024 | β |
| High segregation and diminished global integration in large-scale brain functional networks enhances the perceptual binding of cross-modal stimuli. | Shyamchand Singh S et al. | β | 2024 | β |
| Hippocampus and olfactory impairment in Parkinson disease: a comparative exploratory combined volumetric/functional MRI study. | Porcu M et al. | β | 2024 | β |
| Identification of group differences in predictive anticipatory biasing of pain during uncertainty: preparing for the worst but hoping for the best. | Strigo IA et al. | β | 2024 | β |
| Identifying discriminative features of brain network for prediction of Alzheimer's disease using graph theory and machine learning. | Karim SMS et al. | β | 2024 | β |
| Identifying individual brain development using multimodality brain network. | Jiang Y et al. | β | 2024 | β |
| Identifying subgroups of urge suppression in Obsessive-Compulsive Disorder using machine learning. | Eng GK et al. | β | 2024 | β |
| Identifying the role of (dis)inhibition in the vicious cycle of substance use through ecological momentary assessment and resting-state fMRI. | Chirokoff V et al. | β | 2024 | β |
| Identifying the Shared and Dissociable Neural Bases between Self-Worth and Moral Ambivalence. | Li J et al. | β | 2024 | β |
| Immediate modulatory effects of transcutaneous vagus nerve stimulation on patients with Parkinson's disease: a crossover self-controlled fMRI study. | Fu C et al. | β | 2024 | β |
| Immunomodulatory treatment may change functional and structural brain imaging in severe mental disorders. | Thunberg P et al. | β | 2024 | β |
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| Increased functional connectivity between brain regions involved in social cognition, emotion and affective-value in psychedelic states induced by N,N-Dimethyltryptamine (DMT). | Soares C et al. | β | 2024 | β |
| Increased functional connectivity following ingestion of dried bonito soup. | Satake T et al. | β | 2024 | β |
| Increased functional connectivity of amygdalar-frontal pathways in patients with alcohol use disorder and childhood trauma. | Jehli E et al. | β | 2024 | β |
| Increased interhemispheric functional connectivity after right anodal tDCS in chronic non-fluent aphasia: preliminary findings. | Alemanno F et al. | β | 2024 | β |
| Increases in functional connectivity between the default mode network and sensorimotor network correlate with symptomatic improvement after transcranial direct current stimulation for obsessive-compulsive disorder. | Echevarria MAN et al. | β | 2024 | β |
| Insula-Medial Prefrontal Cortex Functional Connectivity Modulated by Transcutaneous Auricular Vagus Nerve Stimulation: An fMRI Study. | Zhang Y et al. | β | 2024 | β |
| Integrative role of attention networks in frequency-dependent modular organization of human brain. | NeΕe H et al. | β | 2024 | β |
| Interhemispheric functional connectivity: an fMRI study in callosotomized patients. | Marcantoni I et al. | β | 2024 | β |
| Interoceptive training impacts the neural circuit of the anterior insula cortex. | Sugawara A et al. | β | 2024 | β |
| Interpretable prediction of brain activity during conversations from multimodal behavioral signals. | Hmamouche Y et al. | β | 2024 | β |
| Interpretable Spatio-Temporal Embedding for Brain Structural-Effective Network with Ordinary Differential Equation. | Tang H et al. | β | 2024 | β |
| Intrinsic functional connectivity among memory networks does not predict individual differences in narrative recall. | Kurkela K et al. | β | 2024 | β |
| Investigating the bed nucleus of the stria terminalis as a predictor of posttraumatic stress disorder in Black Americans and the moderating effects of racial discrimination. | Petranu K et al. | β | 2024 | β |
| Investigating the effect of hypertension on vascular cognitive impairment by using the resting-state functional connectome. | Hung TH et al. | β | 2024 | β |
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