tracking_open_datasets

tracking_open_datasets#

You can see the full contents of this project on GitHub.

`<Project Name>`#

<1-2 sentences describing the project>

Papers#

How the papers were obtained#

Typically with pubget. We recommend invoking pubget with the --query_file option, and storing a copy of the query file in the project’s directory, or including a copy in the README.md.

<description>

Where the full papers are stored#

Typically on OSF. Please also add a documents/datasets.json file containing the URL where the full pubget dataset can be downloaded, that looks like: [ { "url": "https://osf.io/download/<...>/" } ]

<description>

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/projects/<project_name>/documents/<documents_file2_name>.jsonl
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  - <pubget_folder_name>/subset_allArticles_labelbuddyData/<documents_file2_name>.jsonl

Annotation labels:#

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<label2>: <description of label2>

Labels found in other projects as well:#

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Instructions for annotators#

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Labels in this project#

did not use large open dataset (61 docs)

Example annotations:

…r rfMRI scans from 10 participants and concluded that this intraVar also reflected functionally specialized and flexible configuration across the human brain cerebral cortex [ ]. A recent work on the MyConnectome project [ ] by Poldrack and colleagues has yielded the most detailed depiction of an individual brain’s function across one year (almost daily scanned) [ ], together with the work from Choe and colle…

…als were analyzed. This dataset is published publicly in compliance with Brain Imaging Data Structure (BIDS) specification . All participants recruited in this study previously participated in the studyforrest project ( , , . The T1, T2, SWI structural images and the fMRI dataset for retinotopic mapping, which are available from , have also been utilized in this study. This section provides informatio…

…pecific genes affecting healthy resting-state connectivity must await large datasets with coincident resting-state functional imaging and genotyping. (Genetic data will soon be available both for the HCP and for the UK Biobank imaging data.) Taken together, our results provide strong additional evidence for a neural basis of the heritability of functional connectivity in the human brain. We identif…

…fecting healthy resting-state connectivity must await large datasets with coincident resting-state functional imaging and genotyping. (Genetic data will soon be available both for the HCP and for the UK Biobank imaging data.) Taken together, our results provide strong additional evidence for a neural basis of the heritability of functional connectivity in the human brain. We identify genetic influences bo…

…“good” values of DVARS varies over sites and protocols which makes it difficult to create comparable summaries of data quality across data sets. The emergence of the large scale data sets such as the Human Connectome Project (HCP) ( 1k subjects) and the UK Biobank ( 10k subjects) further motivates the need for automated, yet reliable, quantitative techniques to control and improve the data quality. The purpose of this w…

… which makes it difficult to create comparable summaries of data quality across data sets. The emergence of the large scale data sets such as the Human Connectome Project (HCP) ( 1k subjects) and the UK Biobank ( 10k subjects) further motivates the need for automated, yet reliable, quantitative techniques to control and improve the data quality. The purpose of this work is to provide a formal description …

…different datasets, including task, rest, MEG and fMRI, with potentially thousands of subjects. We anticipate that the generation of large and publicly available datasets from initiatives such as the Human Connectome Project and UK Biobank, in combination with computational methods that can work at this scale, will bring a breakthrough in our understanding of brain function in both health and disease. # Body ## Int…

…ts of neuroimaging data have recently become critical for bridging the gap between basic neuroscience research and clinical applications, such as the diagnosis and treatment of psychiatric disorders (Human Connectome Project [HCP] [ ] [ ]; Human Brain Project [ ]; UK Biobank [ ]; and Strategic Research Program for Brain Sciences [SRPBS] [ ] [ ]) [ – ]. When collecting large amounts of data associated with psychiatric diso…

…g the gap between basic neuroscience research and clinical applications, such as the diagnosis and treatment of psychiatric disorders (Human Connectome Project [HCP] [ ] [ ]; Human Brain Project [ ]; UK Biobank [ ]; and Strategic Research Program for Brain Sciences [SRPBS] [ ] [ ]) [ – ]. When collecting large amounts of data associated with psychiatric disorders, it is necessary to acquire images from mult…

…ing access to population neuroimaging studies, where thousands of fMRI subject data are available, a future study could test for nonzero software‐related variation by splitting a large dataset (e.g., UK Biobank [Alfaro‐Almagro et al., ], N > 10,000) into smaller subsets to generate an extensive collection of replication analyses across the three packages. This may allow for the creation of a null‐distr…

ds - human connectome project (24 docs)

Example annotations:

…d with each other in space and time, a property which we believe is neuroscientifically desirable. We assess the performance of our model on both simulated data and high quality rfMRI data from the Human Connectome Project, and contrast its properties with those of both spatial and temporal independent component analysis (ICA). We show that our method is able to stably infer sets of modes with complex spatio-temporal i…

…state. For both observation models, we simulated state time courses for 200 subjects, with 500 samples per subject. ### fMRI data We used resting-state fMRI data from N = 820 subjects from the HCP, all healthy adults (ages 22–35 years, 453 females) scanned on a 3 T Siemens connectome-Skyra. For each subject, four 15-min runs of fMRI time series data with temporal resolution 0.73 s and spatial …

…m (ds000224) ‘Kirby Weekly’: Downloaded from ‘Day2day’: For availability, see ; section ‘Availability of data and materials’ (available upon request). The 900 subjects release of the Human Connectome Project was used for the cross-sectional dataset. They are downloadable from . For more information on the specific release, see .

…f the findings. In this study, we adopted a method capable of identifying reliable ICNs that can be compared across datasets . The group template of ICNs was identified from two independent datasets (Human Connectome Project [HCP] and Genomics Superstruct Project [GSP]) with large sample sizes ( N = 1005 for GSP and N = 823 for HCP) and different temporal resolutions (see details in Supplementary Note ), and was …

…andon, Jakki and Arichi, Tomoki and Rueckert, Daniel and Hajnal, Joseph V. and Edwards, A. David and Smith, Stephen M. and Duff, Eugene and Andersson, Jesper Neuroimage, 2020 # Title The developing Human Connectome Project (dHCP) automated resting-state functional processing framework for newborn infants # Keywords Developing Human Connectome Project Functional MRI Pipeline Quality control Connectome Neonate # Abst…

…the cumulative biases of pipelines in order to distinguish biological effects from methodological variance. ## Methods Here we use an open structural MRI dataset (ABIDE), supplemented with the Human Connectome Project, to highlight the impact of pipeline selection on cortical thickness measures. Specifically, we investigate the effect of (i) software tool (e.g., ANTS, CIVET, FreeSurfer), (ii) cortical parcellation…

…ation ( ; ). ## Methods ### Data All analyses in the present work were carried out using publicly available datasets selected based on the inclusion of extensive test-retests fMRI. #### Human connectome project (HCP) We made use of the HCP S1200 release dataset ( ; ). The unrelated healthy young adult participants who completed all fMRI scans (i.e. rest and task) were considered in our study. We selecte…

…omplementary to rsfMRI and tfMRI. In this study, functional subdivisions of the cerebellum were parcellated via a dual-regression-like framework based on sparse representation of nfMRI from the Human Connectome Project (HCP). The parcellations were quantitatively evaluated and validated by functional homogeneity and boundary confidence, and quantitatively by comparison between cerebellum–cerebrum functional connect…

…emplate of replicable independent components (ICs) was constructed after spatially matching correlated group-level ICs between two healthy control fMRI datasets—genomics superstruct project (GSP) and human connectome project (HCP). The estimated network template was then used as a prior for a spatially constrained ICA algorithm applied to each UK Biobank subject individually. This identified 53 functionally relevant rest…

…ls while maximally optimizing the unique network property for each subject. The unbiased spatial network templates were estimated using two large independent groups of HCs, that is, 1005 HCs from the Human Connectome Project (HCP) and 823 HCs from the Genomics Superstruct Project (GSP), with the number of independent components (ICs) in ICA set to 100, followed by the selection of 53 reliable, reproducible, and meaningful…

new dataset (20 docs)

Example annotations:

…come critical for bridging the gap between basic neuroscience research and clinical applications, such as the diagnosis and treatment of psychiatric disorders (Human Connectome Project [HCP] [ ] [ ]; Human Brain Project [ ]; UK Biobank [ ]; and Strategic Research Program for Brain Sciences [SRPBS] [ ] [ ]) [ – ]. When collecting large amounts of data associated with psychiatric disorders, it is necessary to acquire …

…sic neuroscience research and clinical applications, such as the diagnosis and treatment of psychiatric disorders (Human Connectome Project [HCP] [ ] [ ]; Human Brain Project [ ]; UK Biobank [ ]; and Strategic Research Program for Brain Sciences [SRPBS] [ ] [ ]) [ – ]. When collecting large amounts of data associated with psychiatric disorders, it is necessary to acquire images from multiple sites because it is nearly impossible for a single …

…n particular will also require larger samples. Increasing sample size and testing sensitivity and specificity across disorders will be greatly facilitated by data-sharing initiatives, including the Pain and Interoception Imaging Network (PAIN) repository, OpenPain (principal investigator: A. Vania Apkarian), UK Biobank, and OpenfMRI. Open data platforms will also aid in the problem of overfitting, making reproducibility, validati…

… sample size and testing sensitivity and specificity across disorders will be greatly facilitated by data-sharing initiatives, including the Pain and Interoception Imaging Network (PAIN) repository, OpenPain (principal investigator: A. Vania Apkarian), UK Biobank, and OpenfMRI. Open data platforms will also aid in the problem of overfitting, making reproducibility, validation, and generalization easier…

…ray–white matter contrast in MR images, our data suggest that it results in apparent cortical thinning. Our findings have broad implications for large-scale studies of brain development including the Pediatric Imaging Neurocognition and Genetics Data Repository ( ), the Adolescent Brain Cognitive Development study ( ), and the HCP data ( ) that use algorithms based on the intensity of MR images to estimate CT. Importantly, since these high-impact and large-…

…ability The following longitudinal datasets were used (and are accessible through): ‘Myconnectome’: Downloaded from (ds000031) ‘The Midnight Scan Club’: Downloaded from (ds000224) ‘Kirby Weekly’: Downloaded from ‘Day2day’: For availability, see ; section ‘Availability of data and materials’ (available upon request). The 900 subjects release of the Human Connectome Project was use…

…al datasets were used (and are accessible through): ‘Myconnectome’: Downloaded from (ds000031) ‘The Midnight Scan Club’: Downloaded from (ds000224) ‘Kirby Weekly’: Downloaded from ‘Day2day’: For availability, see ; section ‘Availability of data and materials’ (available upon request). The 900 subjects release of the Human Connectome Project was used for the cross-sectional dataset…

…a, which is the Cambridge Buckner subset of the 1000 functional connectomes project ( ), and two smaller samples more well suited for test-retest reliability studies. The first small sample being the intrinsic brain activity test retest (IBATRT) dataset ( ), and the second being the midnight scan club (MSC) dataset ( ). For the Cambridge Buckner data sample there were a total of 198 subjects (123 female), ages 18–30 (M = 21.03, SD…

…ved, for fMRI studies that contain large‐scale images of participants and in which sample size is not a considerable concern, like the UK Biobank (Alfaro‐Almagro et al., ) or German National Cohort (German National Cohort, ), the greatest‐motion participants, which account for the greatest effect on FC, can be removed from the group. We suggest that if a group data set is large enough, participants with large motion …

…ne measurement that helps us to bridge the space between biology and behavioral outcomes. Several large-scale studies have employed fMRI to map brain activity in the general population, including the Rotterdam Study (Hofman et al., ), UK Biobank (Miller et al., ), and the Rhineland Study (Breteler et al., ). These large-scale population studies are usually not designed to answer one specific hypothesis. Rathe…

ds - ukbb (15 docs)

Example annotations:

… components = 820 × 4 x 1200 × 50), were standardised so that, for each scan, subject and ICA component, the data have mean 0 and standard deviation 1. We also used resting-state fMRI data from the UK Biobank, a large-scale prospective epidemiological study aiming to allow the identification of risk factors and early biomarkers relating to many diseases ( , , ). We used the first public release containi…

… ### Brain Functional Parcelation We tested four different parcelation maps in order to identify how the number of parcels affects the classification process. Two parcelations were part of the UK Biobank Imaging Study , where about five thousands resting-state functional MRI data points were collected from different participants. Both parcelations were the result of a group independent components ana…

Cole, James H. Neurobiol Aging, 2020 # Title Multimodality neuroimaging brain-age in UK biobank: relationship to biomedical, lifestyle, and cognitive factors # Keywords Brain aging Neuroimaging Multimodality MRI UK Biobank Biomedical measures # Abstract The brain-age paradigm is proving i…

…le size GWAS summary data on chronic pain and sleep disturbance were used to explore their genetic correlations. The GWAS summary data of chronic pain was from a multisite GWAS of chronic pain in the UK Biobank, which included ~380,000 participants . The PSQI is a widely used measure of sleep quality with high sensitivity (98.7%) and specificity (84.4%) for identifying primary insomnia . Because there were…

Leming, Matthew and Suckling, John Neuroimage, 2021 # Title Deep learning for sex classification in resting-state and task functional brain networks from the UK Biobank # Keywords # Abstract Highlights Applied deep learning to sex classification in UK BioBank fMRI connectomes. Deep learning classifies sex better in resting-state than in task fMRI. …

…ional brain networks from big data. sPROFUMO hierarchically estimates fMRI networks for the population and every individual. We characterised high dimensional resting state fMRI networks from UK Biobank. Model outperforms ICA and dual regression for estimation of individual-specific network topography. We demonstrate the model's utility for predicting cognitive traits, and capturing subject …

…ng a Gaussian kernel with FWHM = 6mm. ### 2.3. Group independent component analysis We applied fully automated spatially constrained ICA using the NeuroMark approach [ ] on the 4D preprocessed UK Biobank rs-fMRI data from Section 2.2. In the Neuromark approach, a template of replicable independent components (ICs) was constructed after spatially matching correlated group-level ICs between two healthy…

…ghted MRI, T2-FLAIR, diffusion MRI (dMRI), resting-state functional MRI (fMRI), susceptibility-weighted imaging (swMRI), and arterial spin labelling (ASL), was defined in close approximation to prior UK Biobank (UKB) and C-MORE protocols for Siemens 3T systems. We iteratively defined a comparable set of sequences for General Electric (GE) 3T systems. To assess multi-site feasibility and between-site variabi…

…ivided by the corresponding percentage in the background. The PheWeb database includes genome-wide associations for 1403 EHR-derived ICD billing codes from 408,908 White British participants of the UK Biobank ( ). According to the repository “All individuals were imputed using the Haplotype Reference Consortium panel, resulting in >20 million variants. Analyses on binary outcomes were conducted using SA…

… al., ). ### Network connectivity estimation In constructing functional connectomes, a data‐driven parcellation was obtained from a group‐level ICA in 4000 healthy older participants from the UK Biobank. The original ICA analysis was set at 25 ICs, four of which were considered noise. The 21 signal ICs yielded 210 (i.e., ([21*21] − 21)/2) unique pairwise connections, each of which was examined separ…

ds - adolescent brain cognitive development (14 docs)

Example annotations:

…nd children’s BMI. Methods: For this cross-sectional study, we used functional magnetic resonance imaging (fMRI) data of 6473 9–10-year-old Non-Hispanic Black and Non-Hispanic White children from the Adolescent Brain Cognitive Development (ABCD) study. The primary independent variable was putamen functional connectivity to the salience network, measured by fMRI. The primary outcome was the children’s BMI. Age, sex, neighborhood income…

…es in children with lower levels of PAE with those of well-matched controls with no PAE. ## Design, Setting, and Participants In this cross-sectional study, participants were selected from the Adolescent Brain Cognitive Development study. Children with PAE were compared with controls matched for age, sex, family income, maternal educational level, and caregiver status. Neither group had prenatal exposure to other adverse substa…

…ed mortality. Early intervention in the initial stages of major depressive disorder and bipolar disorder can significantly improve personal health. ## Methods We collected 309 samples from the Adolescent Brain Cognitive Development study, including 116 adolescents with bipolar disorder, 64 adolescents with major depressive disorder, and 129 healthy adolescents, and employed a support vector machine to develop classification mod…

…s have been divided with respect to video gaming’s association with cognitive skills. ## Objective To examine the association between video gaming and cognition in children using data from the Adolescent Brain Cognitive Development (ABCD) study. ## Design, Setting, and Participants In this case-control study, cognitive performance and blood oxygen level–dependent (BOLD) signal were compared in video gamers (VGs) and non–…

…ount for the relationships between cognitive abilities and socio‐demographic, psychological and genetic factors. For this, we leveraged the unique power of the large‐scale, longitudinal data from the Adolescent Brain Cognitive Development (ABCD) study ( n ~ 11 k) and combined MRI data across modalities (task‐fMRI from three tasks: resting‐state fMRI, structural MRI and DTI) using machine‐learning. Our brain‐based, predictive models…

…ciation with cognitive performance in US children. ## Design, Setting, and Participants This cross-sectional study analyzed behavioral and imaging data from 9- to 11-year-old children from the Adolescent Brain Cognitive Development (ABCD) study between August 2017 and November 2018. The ABCD study is an open-science, multisite study following up more than 11 800 youths into early adulthood for 10 years with annual laboratory-ba…

…with diagnosis, treatment monitoring, and response prediction. ## Data availability statement Publicly available datasets were analyzed in this study. This data can be found here: the datasets Adolescent Brain Cognitive Development Study: . ## Ethics statement The studies involving human participants were reviewed and approved by the Ethics Committee of ABCD. Written informed consent to participate in this study was pro…

… prediction of cognitive traits from structural and resting state functional MRI, which seems to account for little behavioral variability. We leverage baseline data from thousands of children in the Adolescent Brain Cognitive Development (ABCD ) Study to inform the replication sample size required with both univariate and multivariate methods across different imaging modalities to detect reproducible brain-behavior associations. We de…

…9 ms, 176 Slices, FOV: 256×256, Voxel Size: 1.0 mm, Bandwidth: 240 Hz/px) image was collected. #### ABCD dataset A large-scale group averaged resting-state functional connectivity map from the Adolescent Brain Cognitive Development (ABCD) study was used to compare individual functional connectivity to averaged group data. This group average map used strict denoising (N = 3,928; >8 min; RSFC data post frame censoring at a filter…

…all studies, as well as large-scale collection efforts with thousands of participants, given competing interests among multiple investigators and limited participant availability. Here, we used the Adolescent Brain and Cognitive Development (ABCD) study and the Human Connectome Project (HCP) to systematically characterize the effects of sample size and scan duration of resting-state fMRI on BWAS prediction accuracy and reliability. We c…

ds - genomics superstruct project (14 docs)

Example annotations:

…rfMRI time series (not normalized), a dual regression (DR) procedure was employed [ ]. Specifically, spatial confidence maps of the seven networks derived from 1,000 healthy adults [ ] of the Brain Genomics Superstruct Project [ ] were employed in the first regression on individual rfMRI images to construct the characteristic time series of the seven networks at individual level in . These characteristic time series wer…

…t al., ). We retrospectively evaluated published video frames showing “lag threads” computed from real BOLD resting state rs-fMRI data in a group of 688 subjects, obtained from the Harvard-MGH Brain Genomics Superstruct Project. We assessed 4 sets of coronal sections (including a total of 54 Images) from the published videos (Threads 1, 2, 3, and 4): We also analyzed 10 well-matched published pairs of networks, from th…

…an inflated form, which facilitates data visualization. We used the fsaverage template from FreeSurfer version 4.5.0. ### Data and FreeSurfer processing Data from 1,490 subjects from the Brain Genomics Superstruct Project (GSP) were considered (Holmes et al., ). All imaging data were collected on matched 3T Tim Trio scanners using the vendor‐supplied 12‐channel phase‐array head coil. Subjects were clinically normal, …

…dopted a method capable of identifying reliable ICNs that can be compared across datasets . The group template of ICNs was identified from two independent datasets (Human Connectome Project [HCP] and Genomics Superstruct Project [GSP]) with large sample sizes ( N = 1005 for GSP and N = 823 for HCP) and different temporal resolutions (see details in Supplementary Note ), and was used as a reference within a spatially …

…ated the effect of two denoising pipelines and different whole‐brain network constructions on reproducibility of subject‐specific graph measures. We used the multi‐session fMRI dataset from the Brain Genomics Superstruct Project consisting of 69 healthy young adults. ## Results In binary networks, the test–retest variability for global measures was large at low density irrespective of the denoising strategy or the typ…

…ion 2.2. In the Neuromark approach, a template of replicable independent components (ICs) was constructed after spatially matching correlated group-level ICs between two healthy control fMRI datasets—genomics superstruct project (GSP) and human connectome project (HCP). The estimated network template was then used as a prior for a spatially constrained ICA algorithm applied to each UK Biobank subject individually. This ident…

…s for each seed (each DBS target) were calculated using a high-quality normative 3 T resting state fMRI data set derived from 1000 healthy subjects (age range: 18–35 years; 57.6% female) of the Brain Genomics Superstruct Project (BGSP, ), as previously described. The MRI acquisition and pre-processing parameters for the BGSP normative connectome are described in detail in the original publication. In short, the data were …

…perty for each subject. The unbiased spatial network templates were estimated using two large independent groups of HCs, that is, 1005 HCs from the Human Connectome Project (HCP) and 823 HCs from the Genomics Superstruct Project (GSP), with the number of independent components (ICs) in ICA set to 100, followed by the selection of 53 reliable, reproducible, and meaningful networks as templates. The network templates can be do…

…nts for the data. These component templates were created via a unified ICA pipeline. They were constructed using an independent resting-state fMRI data with large samples of healthy subjects from the genomics superstruct project (GSP). The GSP data include 1005 subjects’ scans that passed the data QC. High model order (order = 100) group ICA was performed on the GSP data, and then the independent components (ICs) from the GS…

… human RS-fMRI data ( N = 2,010) were obtained from the control arms of primary studies designed, conducted, and analyzed external to the derivative study described herein. These include the Brain Genomics Superstruct Project ( ) (GSP) and ongoing studies at Washington University in St. Louis, including healthy control data from the Alzheimer's Disease Research Center and Neurodegeneration studies ( ). All participants we…

ds - camcan (12 docs)

Example annotations:

…healthy MEG participants completed the task (23 males, mean age 33.7, range 21–41, 4 left-handed) as part of the population-based sample collected by the Cambridge Centre for Ageing and Neuroscience (Cam-CAN, ). Full protocols and exclusion criteria for this cohort are described by . Participants gave written informed consent and ethical approval for the Cam-CAN study was obtained from the Cambridgeshi…

… ). #### Participants ##### Cam-CAN. We used the 253 adults (131 female) who were aged 18–47 (mean age 34.8, SD = 7.9) from the healthy, population-derived cohort tested in Stage II of the Cam-CAN project ( ; ). The majority of participants ( n = 228) were definitively right-handed defined as a handedness measure of ≥50 on a scale of −100 (left) to 100 (right); definitively left-handed were…

…ained Functional connectivity Analysis (DAFA), to deeply mine the important functional connectivity changes in fMRI during brain aging. First, using resting-state fMRI data from 421 subjects from the CamCAN dataset, functional connectivities were calculated using sliding window method, and the complex functional patterns were mined by an AE. Then, to increase the statistical power and reliability of the…

…tworks derived from resting-state fMRI scans of participants from the Cam-CAN project, a study on healthy ageing ( ). ## Methods ### Data The data were collected as part of Phase II of the CamCAN project ( ; ). The MRI data were acquired on a 3T Siemens TIM Trio at the MRC Cognition & Brain Sciences Unit, with a 32 channel head-coil. Structural images were acquired using a 1mm isotropic, T1…

…odel optimization is made with reference to (log)-model evidence, which accounts for both model accuracy and model complexity. We applied DCM to resting-state data from 635 adults aged 18–88 in the CamCAN dataset [ ]. A notable finding was that neural and haemodynamic parameters were independent predictors of age, supporting the hypothesis of separable mechanisms leading to age alterations in neural a…

…ucibility of RSNs in three large independent cohorts comprising a total of 563 older healthy adults (age range: 55–95 years); accordingly, we analyzed data from the Center for Aging and Neuroscience (CamCAN) project ( ; ), the Southwest University Adult Lifespan Dataset (SALD) ( ) and the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database ( ; ); (2) to identify differences in the anatomical c…

…, we applied the same MVB logic to test HAROLD in the context of motor activity related to simple finger presses across two motor fMRI experiments in the Cambridge Center for Ageing and Neuroscience (Cam-CAN) population-derived adult life span sample ( ; ). In experiment 1, participants ( N = 586) pressed a button with their right index finger when they saw/heard a visual/auditory stimulus. In experi…

…ovided an opportunity for the problem we want to study. In this study, we used the resting-state functional magnetic resonance imaging (rs-fMRI) data from Cambridge Center for Aging and Neuroscience (Cam-CAN) database with large sample and long lifespan, and computed the functional connectivity (FC) values for each individual. Based on these values, the hemispheric similarity of functional connectivity (…

…of our study were to: 1) identify the functional gradients of the LC and reproduce them across different cohorts and image resolutions, using a 3T (the Cambridge Centre for Ageing and Neuroscience or CamCAN cohort) and a 7T (the Human Brain Connectome or HCP 7T cohort) datasets; 2) characterize how the functional gradients of the LC change over the course of aging in the CamCAN dataset, a large cohort o…

…hanges in ER accuracy and its association with magnetic resonance imaging (MRI) measures (both structural and functional), on data collected for the ‘The Cambridge Centre for Ageing and Neuroscience (Cam-CAN)’ project ( ; ), with two specific aims. First, to identify when differences in ER performance start to consistently appear along the lifespan. Secondly, across the age groups showing the first sign…

ds - midnight scan club (9 docs)

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…s; TE = 4.77 ms; TI = 1100 ms; voxel size = 1.0 mm × 1.0 mm × 1.0 m; flip angle = 7°). Only the T1-weighted image acquired during the first scan session was used. Dataset 4. The fourth dataset (‘midnight scan club’) contained data from ten subjects (5 females; age range 24–35 years; see, ). Participants were scanned at midnight on twelve consecutive days with a 3T Siemens Trio MRI scanner (Siemens, Erlangen, …

…sults and figures is available at: . ## Data availability The following longitudinal datasets were used (and are accessible through): ‘Myconnectome’: Downloaded from (ds000031) ‘The Midnight Scan Club’: Downloaded from (ds000224) ‘Kirby Weekly’: Downloaded from ‘Day2day’: For availability, see ; section ‘Availability of data and materials’ (available upon request). The 900 subject…

…( ), and two smaller samples more well suited for test-retest reliability studies. The first small sample being the intrinsic brain activity test retest (IBATRT) dataset ( ), and the second being the midnight scan club (MSC) dataset ( ). For the Cambridge Buckner data sample there were a total of 198 subjects (123 female), ages 18–30 (M = 21.03, SD = 2.31), with all subjects included in the final analysis. For th…

…ta, even when using limited amounts of per-subject data, compared to parallel analysis of SE data from the same participants and 14 densely sampled individuals from three SE datasets (n = 10 from the Midnight Scan Club [MSC] [ ]; n = 3 from the Cast-induced Plasticity [CAST] study [ ]; n = 1 from the MyConnectome [MC] project [ ; ]). This effect was linked to at least three biophysical signal mechanisms with spati…

…s relatively low (mean framewise displacement [mean-FD] < 0.2 mm for each of 300 scans, less than 1% [ n = 3] of time points within each scan has FD > 0.2 mm). #### MSC dataset The Midnight Scan Club (MSC) dataset consists of 10 participants, who each participated in 10 fMRI sessions over ten days beginning at midnight ( ) ( ). Each session included 30 mins of resting fMRI using a gradient-echo E…

…oximately 200,000 validation samples (~15,000 per network) were generated from the held out scans. ### 2.6. Testing data After training, model outputs were compared using RS-fMRI data from the Midnight Scan Club ( ) (MSC) collected at Washington University. The MSC contains high quality data collected from 10 participants, each scanned for 30 min in 10 separate sessions. The MSC data are freely avaliable ( )…

…her the coupling nor input signals are directly observable. ### FC Is Related to Shared and Unshared Input Variance in Real fMRI Data To compare communication and FC in empirical data, we used Midnight Scan Club (MSC) dataset ( ), a precision fMRI dataset with 10 sessions of fMRI rest and task data from nine participants. See for BOLD data acquisition, preprocessing, FC, and variance calculation for restin…

…k. As tasks impact signal in a region‐wise fashion, they likely impact FC reliability differently across the brain, making task an important decision in study design. Here, we use the densely sampled Midnight Scan Club (MSC) dataset, comprising 5 h of rest and 6 h of task fMRI data in 10 healthy adults, to investigate regional effects of tasks on FC reliability. We further considered how BOLD signal properties cont…

…mics, two sets of ROIs, and two data sets. Code for computing dynamics of discrete states and their test–retest reliability used in the present paper is available on GitHub [ ]. ## Methods ### Midnight Scan Club data We use the resting-state fMRI data provided by the Midnight Scan Club (MSC) project [ ]. The MSC’s resting-state fMRI data consist of recording from ten healthy human adults [age: (average…

ds - natural scenes dataset (5 docs)

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…unrelated to the experiment. Third, to improve the stability of beta estimates for closely spaced trials, betas are regularized on a voxel-wise basis using ridge regression. Applying GLMsingle to the Natural Scenes Dataset and BOLD5000, we find that GLMsingle substantially improves the reliability of beta estimates across visually-responsive cortex in all subjects. Comparable improvements in reliability are also observ…

… encoding and create personalized synthetic images designed to achieve a targeted pattern of brain activity within a specific individual. ## Materials and methods ### Data description #### Natural Scenes Dataset The individual encoding models were created using the Natural Scenes Dataset (NSD) . The informed consent for all subjects was obtained by NSD. Our data usage was approved by NSD, and complies wi…

… Leveraging the improved sensitivity of modern designs and statistical analyses, we identify two food-selective regions in the ventral visual cortex. Our results are robust across 8 subjects from the Natural Scenes Dataset (NSD), multiple independent image sets and multiple analysis methods. We then test our findings of food selectivity in an fMRI “localizer” using grayscale food images. These independent results confi…

…brain activity; only the free parameters of the read-out heads were optimized to predict brain activity (Fig. c). To optimize the parameters of each type of encoding model (Fig. c, d) we used the Natural Scenes Dataset , a massive sampling of blood-oxygenation-level-depedendent (BOLD) activity in eight subjects using ultra-high field fMRI (7T, 1.8-mm resolution). Subjects each viewed 9000–10,000 natural scenes (sam…

…atterns for viewpoint and depth may differ between static and moving bodies, especially given the complexities of natural image input. ## Materials and Methods ### Stimulus Selection. The Natural Scenes Dataset ( ) contains 73,000 cropped color natural scene images from the MS COCO dataset ( ). We aimed to select a subset of images that contain only single persons and cover a broad range of legitimate human…

ds - myconnectome (3 docs)

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…s for each subject. Altogether, the datasets contained 653 rsfMRI sessions. A summary of the datasets is shown in . Subject information. Table 1 Dataset 1. The first dataset (‘myconnectome’) was part of the MyConnectome project (see, ). During this project, resting state fMRI scans were acquired from a single person (male, 45 years at the start of study) on 89 occasions over the perio…

…ftware availability Code to reproduce analyses, results and figures is available at: . ## Data availability The following longitudinal datasets were used (and are accessible through): ‘Myconnectome’: Downloaded from (ds000031) ‘The Midnight Scan Club’: Downloaded from (ds000224) ‘Kirby Weekly’: Downloaded from ‘Day2day’: For availability, see ; section ‘Availability of data and…

… the same participants and 14 densely sampled individuals from three SE datasets (n = 10 from the Midnight Scan Club [MSC] [ ]; n = 3 from the Cast-induced Plasticity [CAST] study [ ]; n = 1 from the MyConnectome [MC] project [ ; ]). This effect was linked to at least three biophysical signal mechanisms with spatially distinct influences and replicated in two other less densely sampled participants. ## RE…

ds - open access series imaging studies (3 docs)

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… in this study are collected from FBIRN (Function Biomedical Informatics Research Network ) project, from release 1.0 of ABIDE (Autism Brain Imaging Data Exchange ) and from release 3.0 of OASIS (Open Access Series of Imaging Studies ) . Healthy controls from the HCP (Human Connectome Project) ( ) are used for gender prediction. Refer to for details of the datasets. #### Preprocessing We use two typical brain parcellatio…

…ciated with the same network subsystems that mediate the association between Aβ and episodic memory. ## METHODS ### Data Data used in the preparation of this article were obtained from the Open Access Series of Imaging Studies (OASIS) database ( ; accessed: April 4, 2020), collected by the Washington University Knight Alzheimer Disease Research Center over the course of 15 years. Beyond OASIS inclusion criteria, the curren…

…ity non-uniformity (INU) using N4BiasFieldCorrection, ( ) and used as T1w-reference throughout the workflow. The T1w-reference was then skull-stripped using antsBrainExtraction.sh (ANTs 2.2.0), using Open Access Series of Imaging Studies (OASIS) as target template. Brain surfaces were reconstructed using recon-all [FreeSurfer 6.0.1, , ( )], and the brain mask estimated previously was refined with a custom variation of the method to …

ds - southwest university longitudinal imaging multimodal (3 docs)

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…to validate our results in an independent sample to confirm the reliability and repeatability of our study . We tested and validated the main findings in dataset 1 by using an open access dataset [Southwest University Longitudinal Imaging Multimodal (SLIM) Dataset (International Neuroimaging Data-Sharing Initiative (INDI), )] (Liu et al. , ) that also contains rs-fMRI data and SWB measurement in a format identical to that of the behavioral a…

… MRI scans were acquired at baseline and week 12 [ , ]. REST-meta-MDD study consists of resting state fMRI data in medication-naïve first episode and recurrent MDD from 17 sites in China [ , ]. Southwest University (SWU) cohort consists of a community-based recruitment which includes first episode and recurrent MDD and healthy control participants [ – ]. Stanford University cohort consists of MRI data in firs…

…ample of 120 undergraduate students. Then, we unpacked the neuro-cognitive association between insular connectivity and cognitive performance during an Iowa gambling fMRI task. Lastly, an independent Open Southwest University Longitudinal Imaging Multimodal dataset was used to validate the results. Findings suggested that the dAI was predominantly connected to the prefrontal regions; the vAI was primarily connected to the AMG–ventral–striatum system; an…

ds - studyforrest (3 docs)

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…th fMRI scanning of participants viewing films—Stage II of the Cambridge Centre for Aging and Neuroscience (Cam-CAN, ) project (for details, see ) and the 3 T audiovisual movie dataset of the studyforrest ( ) project (for details, see ). #### Participants ##### Cam-CAN. We used the 253 adults (131 female) who were aged 18–47 (mean age 34.8, SD = 7.9) from the healthy, population-derived …

…lly improves the reliability of beta estimates across visually-responsive cortex in all subjects. Comparable improvements in reliability are also observed in a smaller-scale auditory dataset from the StudyForrest experiment. These improvements translate into tangible benefits for higher-level analyses relevant to systems and cognitive neuroscience. We demonstrate that GLMsingle: (i) helps decorrelate response…

… should be noted that the dynamics of the voxel cluster researched in this paper represent the dominant cognitive state dynamics. ### Localizer for higher-visual areas We use the data from the StudyForrest dataset to test whether the locations of VRE-selected voxels are consistent with known functional anatomy, and explore the representation and operations, involved in higher-visual object-selective c…

ds - baby connectome project (2 docs)

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…box is ). In our analysis, fifty three reproducible spatial references, denoted as , were identified by analyzing two distinct fMRI datasets, namely the Genomics Superstruct Project (GSP) and the Human Connectome Project (HCP). The GSP dataset comprises 1005 subjects while the HCP dataset has 823 subjects [ ]. These spatial references were derived using group ICA and are collectively referred to as the Neuromark fMRI…

…subtle, this distinction is worth considering and its implications are worth exploring in future studies. ## METHODS ### Materials. Our subjects were selected from 4 imaging datasets: the Baby Connectome Project (BCP) , and the development, young-adult, and aging cohorts of the Human Connectome Project (HCP-D, HCP-YA, HCP-A) . Subjects in the BCP ranged from 16 days to 6 years old, with 276 subjects (126 mal…

used hcp pipeline (2 docs)

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…lin maps, performs precise within-individual cross-modal registrations, and carries out volume-based registrations to standard spaces. The one-step resampling procedure is a small portion of the full Human Connectome Project (HCP) processing pipeline, which subsequently uses a surface-based approach with numerous further advantages ( ; ; ; ). However, volumetric approaches continue to enjoy widespread popularity as lower resolution fMRI data r…

…ing directions were performed (TR = 7560 ms, TE = 64 ms, FOV = 192 × 192 mm , FA = 90°/180°, matrix size = 96 × 96, 60 slices, slice thickness = 2 mm, and phase partial Fourier = 6/8). To apply the Human Connectome Project (HCP) pipelines to our data, a series of structural images from all subjects were obtained on a day other than the testing day. Two separate sets of T1- and T2-weighted images were acquired using a 3…

ds - bold5000 (1 docs)

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…. Third, to improve the stability of beta estimates for closely spaced trials, betas are regularized on a voxel-wise basis using ridge regression. Applying GLMsingle to the Natural Scenes Dataset and BOLD5000, we find that GLMsingle substantially improves the reliability of beta estimates across visually-responsive cortex in all subjects. Comparable improvements in reliability are also observed in a small…

ds - individual brain charting (1 docs)

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…elcher, David and Pessiglione, Mathias and van Wassenhove, Virginie and Eger, Evelyn and Varoquaux, Gaël and Dehaene, Stanislas and Hertz-Pannier, Lucie and Thirion, Bertrand Sci Data, 2020 # Title Individual Brain Charting dataset extension, second release of high-resolution fMRI data for cognitive mapping # Keywords Brain imaging Cognitive neuroscience Human behaviour Functional magnetic resonance imaging # Abstra…

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