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Functional connectomics from resting-state fMRI
Open accessAbstract
Spontaneous fluctuations in activity in different parts of the brain can be used to study functional brain networks. We review the use of resting-state functional MRI for the purpose of mapping the macroscopic functional connectome. After describing MRI acquisition and image processing methods commonly used to generate data in a form amenable to connectomics network analysis, we discuss different approaches for estimating network structure from that data. Finally, we describe new possibilities resulting from the high-quality rfMRI data being generated by the Human Connectome Project, and highlight some upcoming challenges in functional connectomics.
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TL;DR
This review describes how resting-state fMRI (rfMRI) can map the macroscopic functional connectome, covering acquisition, preprocessing, network modelling, and Human Connectome Project (HCP) data. It highlights high-quality HCP rfMRI enabling detailed node-and-edge connectomes and links to behaviour and sex, while noting major challenges in causality, alignment, and dynamic network modelling.
Key findings
- The HCP is generating rfMRI from over 1000 healthy adults aged 22–35, including twins and non-twin siblings: 1 h of whole-brain 3T rfMRI in two pairs of 15-min runs on separate days, at 2×2×2 mm spatial resolution, 0.7 s temporal resolution, and EPI acceleration factor ×8; over 200 subjects’ datasets were already publicly released, and 3T rfMRI is represented using about 90,000 grayordinates at ~2 mm spacing.
- In the first 131 HCP subjects, aggregating over 600,000 timepoints, group-ICA at dimensionality 100 yielded 98 network nodes after discarding 2 artefactual components; partial correlation matrices were as strong and consistent across subjects as full correlation matrices, which the authors call unusual and indicative of high data quality and many timepoints.
- Multimodal surface matching improved cross-subject network similarity: average between-subject network correlations were FreeSurfer=0.613, MSMfolding=0.618, and MSMmultimodal=0.649; sex prediction with leave-one-out linear discriminant analysis reached 87% for MSMmultimodal versus 78% for FreeSurfer and 82% for MSMfolding, and using full correlation instead of partial correlation reduced sex classification accuracy from 87% to 70%.
- A significant association was found between individual subjects’ network matrices and fluid intelligence, with the 24 strongest edges shown; the node-pair contributing most strongly had only a weak average population connection but varied across subjects in a way that correlated with fluid intelligence. A separate analysis identified 9 edges significantly different in strength between the two sexes.
Methods
- Design: a review of rfMRI-based functional connectomics, including illustrative analyses using publicly released HCP rfMRI data.
- Data/sample: HCP cohort of over 1000 healthy adult twins and non-twin siblings aged 22–35; the illustrative analyses used the first 131 subjects’ rfMRI data, aggregating over 600,000 timepoints.
- Main analysis: preprocessing with FSL, FreeSurfer, and Connectome Workbench; ICA-based artefact removal with FIX (reported >99% classification accuracy on HCP data); group-ICA at dimensionality 100 yielding 98 nodes; full and partial correlation, regularised inverse covariance, multimodal surface matching, permutation testing, linear discriminant analysis, and temporal-ICA.
Limitations
- Stated in paper: correlation cannot reveal causality or whether connectivity is direct versus indirect; partial correlation estimates direct connections but not directionality; directionality estimation is harder than edge detection, temporal lag is confounded by slow and variable haemodynamics, and observational rfMRI is not a robust tool for inferring causality compared with interventional task-fMRI.
- Stated in paper: dynamic causal modelling is practical only for networks with fewer than 10 nodes; for 50–500 nodes, partial correlation is a pragmatic compromise but inverse covariance estimation is often unstable and benefits from regularisation; graph-theory measures risk inappropriate node definitions, use of thresholded full correlation matrices, and confounds such as head motion or heart rate.
- Stated in paper: temporal-ICA forces modes to be fully independent over time, assumes within-mode connection strengths are static, and cannot well identify mutually exclusive modes with negative correlation; sliding-window correlation can be confounded by window length and overlapping networks; no single parcellation technique has emerged as best; and larger heterogeneous datasets such as the Thousand Functional Connectomes have greater scanning-parameter heterogeneity and lower data quality than HCP. Evident from text: the paper is a review with illustrative HCP analyses rather than a single primary empirical study, so its quantitative results are presented as examples of methodological potential and issues.
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50 Own interpretation · 42 Not checked yet · 12 Own result · 11 No basis given · 1 Partly supported · accuracy not yet measured
In the paper
“Significant improvements in the alignment of task activation regions were found, both quantitatively and qualitatively [Robinson, in submission];”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [Robinson, in submission]
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“When MSM is only given folding information to drive the alignment (“MSMfolding”), the overall degree of alignment is similar to that achieved by FreeSurfer.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“for example, Figure 5B shows stronger and more sharply defined activation patterns from a group-level analysis of two different tasks (“maths vs story” and a social interaction task) when MSMmultimodal is utilised (lower panels) compared to MSMfolding (upper panels), especially in parts of prefrontal cortex (blue arrows).”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
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In the paper
“When we used the full correlation network matrices instead of partial correlation, the sex classification accuracy was reduced from 87% to 70%.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“However, if MSM is also fed cortical myelin-weighted maps [76], as well as low-dimensional resting-state network maps, it can utilise richer structural and connectional information, and further improve the intersubject alignment (“MSMmultimodal”) [43].”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not matchedcites [76] Glasser MF 2011 Comparison of Surface Gradients Derived from Myelin Maps and Functional Connectivity Analysis Int. Conf. on Functional Mapping of the Human Brain
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Not checked yetcites [43] Glasser MF 2013 The Minimal Preprocessing Pipelines for the Human Connectome Project NeuroImage 80 105 124 23668970 PMC3720813 source
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In the paper
“Using leave-one-out training and testing, sex was successfully predicted in 87% of subjects”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
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In the paper
“This identified 9 edges that were significantly different in strength between the two sexes.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“In Figure 7, we utilise the above approach to show a significant association between individual subjects’ network matrices and fluid intelligence (a component of IQ).”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
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In the paper
“Notably, the overall range of values is similar for both matrices.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
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In the paper
“and are consistent across subjects [4]”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [4] Yeo BT 2011 The organization of the human cerebral cortex estimated by intrinsic functional connectivity J Neurophysiol 106 1125 1165 21653723 PMC3174820 source
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In the paper
“the study of RSNs has already been shown to have potential clinical value, providing rich and sensitive markers of disease [8]”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [8] Castellanos FX 2013 Clinical applications of the functional connectome Neuroimage 80 527 540 23631991 PMC3809093 source
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In the paper
“it was first noted that the rfMRI timeseries from one part of the motor cortex were temporally correlated with other parts of the same functional network, even with the subject at rest [1]”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [1] Biswal B 1995 Functional Connectivity in the Motor Cortex of Resting Human Brain Using Echo-Planar MRI Magnetic Resonance in Medicine 34 537 541 8524021 source
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In the paper
“and, to some extent, across species [5]”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [5] Li L 2013 Mapping putative hubs in human, chimpanzee and rhesus macaque connectomes via diffusion tractography Neuroimage 80 462 474 23603286 PMC3720835 source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“a detailed network modelling facilitates analysis of both functional specialisation (investigating the functional connectivities of each node separately), and functional integration (investigating how nodes interact with each other, and form communities of functionally-related clusters of nodes).”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
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In the paper
“Higher temporal resolution of the fMRI data can improve overall statistical sensitivity”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
What the sources say
- Not checked yetcites [41] Feinberg DA 2010 Multiplexed Echo Planar Imaging for Sub-second Whole Brain FMRI and Fast Diffusion Imaging PLoS ONE 5 e15710 21187930 PMC3004955 source
- Not checked yetcites [42] Smith SM 2012 Temporally-independent functional modes of spontaneous brain activity Proc Natl Acad Sci USA (PNAS) 109 3131 3136 PMC3286957 22323591 source
plainconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“A common implicit assumption, that correlation is unambiguously indicative of a direct connection, creates a major problem for network modelling (and graph theory applied to networks estimated from rfMRI) [35].”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [35] Smith SM 2012 The Future of FMRI Connectivity NeuroImage 62 1257 1266 22248579 source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The fMRI acquisition is tuned such that the image intensity reflects local blood flow and oxygenation changes resulting from variations in local neural activity [37].”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
What the sources say
- Not checked yetcites [37] Ogawa S 1992 Intrinsic Signal Changes Accompanying Sensory Stimulation: Functional Brain Mapping with Magnetic Resonance Imaging Proc Natl Acad Sci USA 89 13 5951 5955 1631079 PMC402116 source
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In the paper
“The simplest method, correlation between the timecourses of any two brain regions, allows one to infer whether the regions are functionally “connected””
§ Functional connectomics from resting-state fMRI > Functional network modelling
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In the paper
“many factors other than the direct anatomical node-to-node connection “true strength” can affect correlation coefficients, including variations in signal amplitude and noise level [48].”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [48] Friston KJ 2011 Functional and effective connectivity: A review Brain Connectivity 1 13 36 22432952 source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Early rfMRI studies typically characterised functional connectivity via a small number of large-scale spatial maps [1, 2].”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [1] Biswal B 1995 Functional Connectivity in the Motor Cortex of Resting Human Brain Using Echo-Planar MRI Magnetic Resonance in Medicine 34 537 541 8524021 source
- Not checked yetcites [2] Beckmann CF 2005 Investigations into Resting-State Connectivity using Independent Component Analysis Philosophical Transactions of the Royal Society 360 1001 1013 PMC1854918 16087444 source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“It is now generally accepted not only that RSNs do reflect networks of brain function [10]”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [10] Sadaghiani S Kleinschmidt A 2013 Functional interactions between intrinsic brain activity and behavior Neuroimage 80 379 386 23643921 source
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In the paper
“there is increasing evidence that there is useful signal at relatively high frequencies [47].”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
What the sources say
- Not checked yetcites [47] Niazy RK 2011 Spectral characteristics of resting state networks Elsevier 21854968 source
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In the paper
“Although there has been concern that some patterns of spatially-extended spontaneous signals may be of non-neural physiological origin, these concerns are increasingly being addressed [9].”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [9] Murphy K 2013 Resting-state fMRI confounds and cleanup Neuroimage 80 349 359 23571418 PMC3720818 source
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In the paper
“the extensive set of functional networks identified in the task-fMRI literature (e.g., as encoded into the BrainMap meta-analysis database [11]), can be found in rfMRI data [12].”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [12] Smith SM 2009 Correspondence of the brain’s functional architecture during activation and rest Proc Natl Acad Sci USA (PNAS) 106 13040 13045 PMC2722273 19620724 source
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In the paper
“The directionality of edges (causality) is often investigated, but in general it is harder to estimate the direction of a connection from fMRI data than to detect whether an edge exists [56].”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [56] Smith SM 2011 Network Modelling Methods for FMRI NeuroImage 54 875 891 20817103 source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“However, simpler methods provide descriptions of the data, rather than being directly tied to underlying, more biologically interpretable, network parameters.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“dominant average causalities found from rfMRI may not relate meaningfully to the route by which information flows around the “brain network” when triggered by distinct external events.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
hedged- Asserted: passes — The authors put it forward as true.
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In the paper
“A further complication arises if brain activity in one region modulates the connections strengths between other nodes. This renders analyses based on assumptions of linearity inaccurate”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, this is currently practical (in terms of both computational expense and mathematical robustness) only for networks with a small number of nodes (<10).”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Non-Gaussianities in the timeseries [60, 61] provide a distinct, potentially valuable source of causality information.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [60] Patel RS 2006 A Bayesian Approach to Determining Connectivity of the Human Brain Human Brain Mapping 27 267 276 16092131 PMC6871439 source
- Not checked yetcites [61] Hyvarinen A Smith SM 2013 Pairwise Likelihood Ratios for Estimation of Non-Gaussian Structural Equation Models Journal of Machine Learning Research 14 111 152 PMC6834441 31695580
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“if inter-subject alignment of rfMRI data is only driven by information from high resolution structural images, it is expected that alignment of cortical functional areas across subjects will be imperfect in many regions, given the variable relationship between cortical areas and structural features such as tissue intensities and cortical folding patterns [69].”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [69] Van Essen DC 2012 Parcellations and hemispheric asymmetries of human cerebral cortex analyzed on surface-based atalses Cerebral Cortex 22 2241 2262 22047963 PMC3432236 source
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In the paper
“Hence, improved estimation can often be achieved by “regularising” the estimated inverse covariance matrix.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plainconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“the HCP has developed a method for multimodal intersubject alignment, capable of using many sources of spatial localisation information, including geometric structural features, myelin-weighted images, task-fMRI maps and connectivity information (from rfMRI and diffusion MRI) [70].”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [70] Robinson E 2013 Multimodal Surface Matching: Fast and Generalisable Cortical Registration using Discrete Optimisation Springer Berlin Heidelberg 24683992
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In the paper
““observational data” (such as rfMRI) is in general not a robust and safe tool for inferring causality, compared with “interventional” studies (such as task-fMRI experiments) [63].”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [63] Pearl J 2009 Causal inference in statistics: An overview Statistics Surveys 3 96 146 source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“In recent work involving networks of simulated fMRI timeseries with up to 50 nodes, such methods performed the most accurately [56].”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [56] Smith SM 2011 Network Modelling Methods for FMRI NeuroImage 54 875 891 20817103 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the simpler methods can handle a much larger number of network nodes than the more complex methods”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“These methods also scale well, handling hundreds of nodes given sufficient data (primarily, a large number of timepoints).”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“One specific risk is the use of inappropriate node definition [56, 66], such as a gross structural atlas-based parcellation that corresponds poorly to functional boundaries and results in network matrices whose neurobiological interpretability is limited”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Because the majority of brain connections are bi-directional [62]”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [62] Markov N 2013 A Weighted and Directed Interareal Connectivity Matrix for Macaque Cerebral Cortex Cerebral Cortex 10.1093/cercor/bhs270 PMC3862262 23010748
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The smaller the individual parcels (node maps), the more crucial it becomes to address this problem.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“There is not necessarily a relationship between the strength (or even sign) of the population average connection between two nodes and the extent to which the cross-subject variability in the connection strength correlates with a given behavioural measure.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Once a “timeseries of correlation matrices” has been generated through sliding-window correlation, clustering analysis can be used to identify distinct correlation patterns that repeatedly re-appear over an extended period [88].”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [88] Hutchison RM 2013 Dynamic functional connectivity: Promise, issues, and interpretations Neuroimage 80 360 378 23707587 PMC3807588
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“If the overall model fit is found to be significant, it provides evidence for a link between the functional connectome and a specific behavioural characteristic.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“however, Bonferroni correction would likely be conservative, because we do not expect the subject-wise variations of all edges to be fully independent of each other.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: The subject-wise variations of all edges are not fully independent of each other.
In the paper
“Recent evidence [47] indicates that resting-state network signals occur up to at least 0.2Hz in good quality data;”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [47] Niazy RK 2011 Spectral characteristics of resting state networks Elsevier 21854968 source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The fact that some connections are stronger in females than in males, and some are weaker, suggests that the discrimination is not driven primarily by uninteresting gross effects such as group biases in head size or within-scan head motion.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Removal of the artefact components from the data is then carried out, improving data quality.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This supports the hypothesis that partial correlation matrices provide a better estimate of the “true” macroscopic functional connectome than full correlation.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: There is a true macroscopic functional connectome that partial correlation matrices estimate better than full correlation.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Different methods for aligning data across subjects can be partially evaluated by estimating how similar the resulting network matrices are to each other.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This technique thus benefits greatly from long rfMRI sessions and accelerated acquisition, such as that obtained by the HCP.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
boosteddirectn = 131- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The macroscopic functional connectome as elucidated through resting-state functional MRI provides just one view on the “complete” brain connectome.”
§ Functional connectomics from resting-state fMRI > Conclusions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“One limitation of temporal-ICA is that all modes are forced to be fully independent of each other over time;”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“A major challenge for temporal-ICA, however, is the need for a large number of timepoints to perform robustly.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“If that is the case, windowed correlation patterns may not be very informative, because distinct overlapping and co-activating networks’ varying amplitudes will play a large factor in the apparent correlation pattern, confounding estimation of their “true” distinct internal connectivities.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Probably not a substantial claim. 23
- It may state two separate claims as one. 45
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
““multiband accelerated EPI” acquires multiple slices simultaneously [39, 40]. Such approaches enable major improvements in spatial and/or temporal resolution, for example acquiring data with 2mm spatial resolution in less than a second.”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
What the sources say
- Partly supportedcites [39] Moeller S 2010 Multiband multislice GE-EPI at 7 tesla, with 16-fold acceleration using partial parallel imaging with application to high spatial and temporal whole-brain fMRI Magn Reson Med 63 1144 1153 20432285 PMC2906244 sourceExperimental — accuracy not yet measured
The Abstract and Results (Functional Imaging) show that multiband EPI acquired multiple slices simultaneously and achieved 2 × 2 × 2 mm³ whole-brain fMRI. The reported repetition time for that acquisition was 1.25 seconds, not less than a second, so the speed in the example is not supported. (LLM, conf=0.90)
- Supportedcites [40] Setsompop K 2012 Blipped-controlled aliasing in parallel imaging for simultaneous multislice echo planer imaging with reduced g-factor penalty Magnetic Resonance in Medicine 67 1210 1224 21858868 PMC3323676 source
The Introduction says simultaneous acquisition of multiple slices directly reduces the time needed to acquire a fixed number of slices. The Methods > Acquisitions passage reports 2-mm isotropic resolution with a TR of 0.77 s, and the Discussion and Conclusion explicitly describes 2-mm isotropic whole-brain coverage in 0.77 s. (LLM, conf=0.94)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Partly supported
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Indeed, the histogram of edge-strength mean group differences is centred at zero, with no gross asymmetry.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We found the following average correlation values for the 3 alignment methods: FreeSurfer=0.613, MSMfolding=0.618 and MSMmultimodal=0.649 (Figure 5A).”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Indeed, the node-pair which contributes most strongly to the regression against fluid intelligence (shown in more detail in B) has only a weak connection on average in the population - but it varies across subjects in a way that correlates with fluid intelligence.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The 3 alignment methods described above gave classification accuracies of: FreeSurfer=78%, MSMfolding=82% and MSMmultimodal=87%.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The 24 edges (node-pairs) having the strongest weights in the regression are shown;”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In both cases we show strong spatial correspondence to specific task activation maps from the HCP task-fMRI datasets, thus helping to provide interpretation for the functional modes identified from the resting-state data.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Figure 9 shows 2 example results from feeding 98 nodes’ timeseries into temporal-ICA, where we analysed the high quality HCP rfMRI data containing more time points (>600,000, concatenating data from 131 subjects) than spatial points (~90,000 grayordinates).”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plainn = 131- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“These patterns can be distinguished from each other because, while each has a relatively consistent timecourse across its set of involved regions, the different networks have distinct timecourses [2].”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [2] Beckmann CF 2005 Investigations into Resting-State Connectivity using Independent Component Analysis Philosophical Transactions of the Royal Society 360 1001 1013 PMC1854918 16087444 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“These “resting-state networks” (RSNs) persist even during sleep and under anaesthesia [3]”
§ Functional connectomics from resting-state fMRI > Resting-state fMRI and the connectome – what’s the connection?
What the sources say
- Not checked yetcites [3] Picchioni D 2013 Sleep and the functional connectome Neuroimage 80 387 396 23707592 PMC3733088 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Such an approach contains fine spatial detail, but only informs about average correlation with the selected seed(s).”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Effective artefact removal is particularly important for resting-state analyses, which rely fundamentally on correlations between different voxels’ timeseries, as these will be corrupted by artefacts that span multiple voxels.”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“a high-dimensional parcellation into many nodes (potentially hundreds) allows a richer analysis of the network connections – by shifting the emphasis from large-scale maps with fine spatial detail into a network description of “nodes” and “edges”, new information can be obtained.”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“although the sluggish response of the brain’s haemodynamics (to neural activity) will ultimately place a limit on the usefulness of further improvements in temporal resolution.”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“(In contrast, task-fMRI has the advantage of fitting a pre-specified temporal model, which provides greater robustness against artefactual influences.)”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“accurate alignment of functionally corresponding cortical parcels is an exceedingly challenging problem, largely owing to individual variability of cortical folding patterns along with variability of functional parcel locations relative to these folds”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In order to combine or compare connectomes across subjects, it is important to strive for “the same” parcellation in each subject – comparisons between two network models are inherently flawed if they are derived from non-corresponding sets of nodes.”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“and also increase the information content of the data (e.g., in terms of reflecting the richness of the neural dynamics) [41, 42]”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
What the sources say
- Not checked yetcites [41] Feinberg DA 2010 Multiplexed Echo Planar Imaging for Sub-second Whole Brain FMRI and Fast Diffusion Imaging PLoS ONE 5 e15710 21187930 PMC3004955 source
- Not checked yetcites [42] Smith SM 2012 Temporally-independent functional modes of spontaneous brain activity Proc Natl Acad Sci USA (PNAS) 109 3131 3136 PMC3286957 22323591 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“a detailed nodes+edges network model may reveal which nodes (sub-parts of the large-scale networks) are responsible for the correlations seen between the larger-scale networks.”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“Furthermore, correlation cannot reveal anything about causality, or even whether connectivity is direct vs indirect [49].”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [49] Marrelec G 2006 Partial correlation for functional brain interactivity investigation in functional MRI NeuroImage 32 228 237 16777436 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This therefore generates a richer description of multiple networks in the brain, but at the expense of no longer dictating in advance the regions with which the connectivity map(s) are related.”
§ Functional connectomics from resting-state fMRI > rfMRI acquisition and image processing overview
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For example, in a 3-node network A→B→C, all three nodes’ timeseries will be correlated, so correlation will incorrectly estimate a fully-connected network (including an A-C connection).”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“while DCM, originally developed for task data, has recently been extended [54] to allow modelling of resting-state data, and to search across a wide range of possible network matrix models”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [54] Friston KJ 2011 Network discovery with DCM NeuroImage 56 1202 1221 21182971 PMC3094760 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“L1-norm regularisation of the inverse covariance matrix [55] shrinks the estimated values in the partial correlation matrix, so that very small, noisy values are forced to zero, and all other values are better estimated.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [55] Friedman J 2008 Sparse inverse covariance estimation with the Graphical Lasso Biostat 9 432 441 PMC3019769 18079126 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Naturally, these techniques are dependent on accurate network modelling at the lower level (carefully constructed network matrices); the abstraction of these metrics from the underlying data makes it challenging to evaluate results”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The HCP is generating a detailed in vivo mapping of functional connectivity in a large cohort (over 1000 subjects), and is making these datasets freely available for use by the neuroimaging community (over 200 subjects’ datasets are already acquired and publicly released – available via humanconnectome.org).”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plainn = 200- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Bayes nets model the full set of covariances (or conditional dependencies) between all nodes’ timeseries [59] and show some promise.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [59] Ramsey JD 2010 Six problems for causal inference from fMRI NeuroImage 49 1545 1558 19747552 source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Another concern is that it is frequently the (thresholded) full correlation matrix that is input into graph theoretical analyses, rather than an estimate of direct network connections; interpretations of graph-theory-based measures (such as communication path length) are often, as a result, somewhat questionable.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Many methods, such as correlation, give no directionality information at all.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This growing dataset comes with the caveat of having greater heterogeneity of scanning parameters (and lower data quality) than the HCP”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“another simple estimation method, partial correlation, aims to more accurately estimate the “direct” connections (though not their directionalities).”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The MGH-UCLA HCP is using extremely powerful MRI gradients to generate leading-edge 3T diffusion MRI data.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [16] Setsompop K 2013 Pushing the limits of in vivo diffusion MRI for the Human Connectome Project Neuroimage 80 220 233 23707579 PMC3725309 source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“it cannot be assumed that the brain’s connections are static.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“the WashU-UMinn-Oxford (“WU-Minn”) HCP is generating high quality and high resolution 3T rfMRI and diffusion MRI data from over 1000 healthy adults, as well as task-fMRI, genotyping and behavioural data.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [67] Van Essen DC 2013 The WU-Minn Human Connectome Project: An Overview NeuroImage 80 62 79 23684880 PMC3724347 source
plainn = 1,000- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In this case, regression of B out of A and C removes the correlation between A and C, and hence the spurious third edge (A–C).”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The simpler methods are in general more robust (with respect to fitting the model to the data), and faster to compute.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“they do not require the scope of possible network models to be pre-constrained, making them computationally feasible for attempting network discovery.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Subjects are drawn from a population of healthy adult twins and their non-twin siblings (in the age range of 22–35 years), thus aiding the study of the influence of heritability and environmental factors on the connectome.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Temporal lag between pairs of timeseries [58] is often used, though it is arguably too confounded by the slow and variable haemodynamics to be useful with fMRI data [56], and is better-suited to electrophysiological modalities.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
What the sources say
- Not checked yetcites [56] Smith SM 2011 Network Modelling Methods for FMRI NeuroImage 54 875 891 20817103 source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The estimation of partial correlation effectively involves inverting the full correlation matrix, a process which is often quite unstable, depending on the quality of the data and the number of original timepoints.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“causality estimation when the brain is “at rest” may involve many different functional processes mixed together, and would be estimated as the average “relative causality” over all possible spontaneous fluctuations.”
§ Functional connectomics from resting-state fMRI > Functional network modelling
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The Thousand Functional Connectomes (and related) projects [74, 75], led by Mike Milham, are seeking to generate even larger numbers of subjects than the HCP, bringing together data from a wide range of imaging studies and scanners, and covering a wider range of subject groups, including a range of pathologies.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [74] Biswal BB 2010 Towards discovery science of human brain function Proc Natl Acad Sci USA (PNAS) 107 4734 4739 PMC2842060 20176931 source
- Not checked yetcites [75] Yan CG 2013 Standardizing the intrinsic brain: Towards robust measurement of inter-individual variation in 1000 functional connectomes Neuroimage 80 246 262 23631983 PMC4074397 source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Once each subject’s cortical surface has been estimated from the structural data using FreeSurfer, FreeSurfer also provides one way to improve intersubject alignment of features on the surface.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For the partial correlation matrices to be as strong and consistent across subjects as the full correlation is unusual and is indicative of the high quality of the data and large number of timepoints in each subject’s rfMRI dataset.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This suggests that multimodal MSM improves the alignment of function across subjects (as it improves the accuracy with which the derived network matrices can predict sex), and also supports the hypothesis that this sex prediction is indeed primarily being driven by network connection strength and not (for example) by systematic functional misalignments across (groups of) subjects.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“This kind of analysis has previously been used (albeit from full correlation network matrices) to predict subjects’ psychiatric condition [77] and cognitive state [78];”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [77] Craddock RC 2009 Disease state prediction from resting state functional connectivity Magnetic Resonance in Medicine 62 1619 1628 19859933 PMC3749911 source
- Not checked yetcites [78] Shirer WR 2012 Decoding subject-driven cognitive states with whole-brain connectivity patterns Cereb Cortex 22 158 165 21616982 PMC3236795 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“One important issue is to distinguish between changes in correlation due to some nodes being part of multiple overlapping functional networks, vs. the internal connections within any given network being non-constant.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“We have recently developed an alternative surface warping approach, Multimodal Surface Matching (MSM) [70].”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [70] Robinson E 2013 Multimodal Surface Matching: Fast and Generalisable Cortical Registration using Discrete Optimisation Springer Berlin Heidelberg 24683992
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In addition, a problem can arise when applying a window length that does not encompass (at least) several cycles of the resting fluctuations, as the rfMRI signal is dominated by low frequencies (~0.015Hz), and a sliding window containing a fraction of a cycle is expected to show correlations appearing to fluctuate wildly over time, even if the underlying network structure is stationary.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plainconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: The rfMRI signal is dominated by low frequencies (~0.015Hz).
In the paper
“FIX achieves classification accuracy on HCP data of over 99%.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites Salimi-Khorshidi, unpublished manuscript
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“At this point, no single parcellation technique has emerged as the best approach, and investigations are ongoing.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, better alignments should yield more accurate network matrices, because the functional parcels defined at the group level should be more accurately aligned to the true subject-specific versions of those same parcels.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- Rests on an assumption: The functional parcels defined at the group level correspond to true subject-specific versions of those same parcels.
In the paper
“For example, nonstationarities in correlation have been studied utilising either wavelet decompositions or sliding-window correlation [88].”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [88] Hutchison RM 2013 Dynamic functional connectivity: Promise, issues, and interpretations Neuroimage 80 360 378 23707587 PMC3807588
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, although this is encouraging, an increase in cross-subject network similarity is not conclusive proof of a better alignment method; for example, it might indicate over-strong application of prior information (e.g., in the extreme, setting all subjects to a constant network), which would reduce sensitivity when attempting to relate the network matrices to other measures.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A limitation, however, is that multiple distinct functional networks might overlap each other in space and also vary over time in how they interact with each other.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“It does not provide the more direct view of neuronal activity and information flow that can be obtained from electrophysiological techniques, or inform us regarding the biochemistry of brain connectivity.”
§ Functional connectomics from resting-state fMRI > Conclusions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“[42] showed several such modes, with plausible functional interpretability and large amounts of spatial overlap; for example, the patterns of average correlation and anti-correlation associated with the default-mode network can be decomposed into several modes of distinct but overlapping spatial layout (and hence presumably distinct function).”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [42] Smith SM 2012 Temporally-independent functional modes of spontaneous brain activity Proc Natl Acad Sci USA (PNAS) 109 3131 3136 PMC3286957 22323591 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“A related challenge is raised by evidence that rfMRI signal includes complex spatiotemporal patterns of spontaneous activity that propagate across the brain [92], and are therefore not at all well modelled by spatially fixed network modelling approaches.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
What the sources say
- Not checked yetcites [92] Majeed W 2010 Spatiotemporal dynamics of low frequency BOLD fluctuations in rats and humans Neuroimage 54 1140 1150 20728554 PMC2997178
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, rfMRI does provide us with something valuable and unique – the ability to create a richly detailed mapping of the functional connectome, at the millimetre scale, covering the whole brain, with in vivo, non-invasive imaging across thousands of subjects.”
§ Functional connectomics from resting-state fMRI > Conclusions
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: unclear — It is unclear why the paper says it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“It does not tell us directly about the microscopic, neuronal-level, structural connectome, or even about the macroscopic-level structural connectome such as is inferred from diffusion MRI.”
§ Functional connectomics from resting-state fMRI > Conclusions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Another limitation with temporal-ICA is the assumption that the connections within a given mode are not changing in strength over time; this is surely an oversimplistic view of brain networks.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For example, two distinct functional modes might in reality be mutually exclusive, if they share one node that strongly participates in only one function at any given time; this would imply a negative correlation between the modes’ timeseries, and this situation will not be well identified through the application of temporal-ICA.”
§ Functional connectomics from resting-state fMRI > The Human Connectome Project and future directions for macroscopic functional connectomics
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper relies on this without support.
The biological significance of the rich and continuously-present set of spontaneous, correlated activities in the resting brain remains poorly understood.
“The biological significance of such a rich and continuously-present set of spontaneous, correlated activities in the “resting” brain remains poorly understood.”
The authors state this as an assumption.
The brain is continuously engaged in undirected cognitive activities, including conscious thought processes and sub-conscious activity such as learning/unlearning, and also responds to uncontrolled external stimuli.
“Presumably, the brain is continuously engaged in undirected cognitive activities (both conscious thought processes and sub-conscious activity such as learning/unlearning), and also responds to uncontrolled external stimuli.”
The paper relies on this without support.
The functional parcels defined at the group level correspond to true subject-specific versions of those same parcels.
“because the functional parcels defined at the group level should be more accurately aligned to the true subject-specific versions of those same parcels.”
The paper relies on this without support.
The subject-wise variations of all edges are not fully independent of each other.
“because we do not expect the subject-wise variations of all edges to be fully independent of each other.”
The paper relies on this without support.
The rfMRI signal is dominated by low frequencies (~0.015Hz).
“as the rfMRI signal is dominated by low frequencies (~0.015Hz)”
The paper relies on this without support.
There is a true macroscopic functional connectome that partial correlation matrices estimate better than full correlation.
“partial correlation matrices provide a better estimate of the “true” macroscopic functional connectome than full correlation.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Functional connectivity as measured using fMRI is a powerful but indirect measure of network organization that can provide high spatial resolution but should not be considered a surrogate for direct anatomical connectivity29, 30.”
From Canonical genetic signatures of the adult human brain (2015) · cites this paper as [30]
In the citing paper
“Each of four 15-min resting state runs for each subject in the group was cleaned (denoised) using 24-parameter motion regression followed by ICA+FIX denoising30, 48.”
From Canonical genetic signatures of the adult human brain (2015) · cites this paper as [30]
Citations
Cites
Investigating causal relations by econometric models and cross-spectral methods
Granger, C. W. J. (1969) · Econometrica · doi:10.2307/1912791 · Cited by 22,989
Complex network measures of brain connectivity: Uses and interpretations
Rubinov, M., & Sporns, O. (2010) · NeuroImage · doi:10.1016/j.neuroimage.2009.10.003 · Cited by 11,522
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Self-citationFunctional connectivity in the motor cortex of resting human brain using echo‐planar mri
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Fischl, B. (2012) · NeuroImage · doi:10.1016/j.neuroimage.2012.01.021 · Cited by 9,526
The organization of the human cerebral cortex estimated by intrinsic functional connectivity
Thomas Yeo, B. T., Krienen, F. M., Sepulcre, J., Sabuncu, M. R., Lashkari, D., Hollinshead, M., Roffman, J. L., Smoller, J. W., Zöllei, L., Polimeni, J. R., et al. (2011) · Journal of Neurophysiology · doi:10.1152/jn.00338.2011 · Cited by 9,182
Power, J. D., Barnes, K. A., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2012) · NeuroImage · doi:10.1016/j.neuroimage.2011.10.018 · Cited by 7,429
The organization of the human cerebellum estimated by intrinsic functional connectivity
Buckner, R. L., Krienen, F. M., Castellanos, A., Diaz, J. C., & Yeo, B. T. T. (2011) · Journal of Neurophysiology · doi:10.1152/jn.00339.2011 · Cited by 7,304
Sparse inverse covariance estimation with the graphical lasso
Friedman, J., Hastie, T., & Tibshirani, R. (2008) · Biostatistics · doi:10.1093/biostatistics/kxm045 · Cited by 6,355
The WU-Minn Human Connectome Project: An overview
Van Essen, D. C., Smith, S. M., Barch, D. M., Behrens, T. E. J., Yacoub, E., & Ugurbil, K. (2013) · NeuroImage · doi:10.1016/j.neuroimage.2013.05.041 · Cited by 5,651
Self-citation
Cited by
Sorted by citations
A multi-modal parcellation of human cerebral cortex
Glasser, M. F., Coalson, T. S., Robinson, E. C., Hacker, C. D., Harwell, J., Yacoub, E., Ugurbil, K., Andersson, J., Beckmann, C. F., Jenkinson, M., et al. (2016) · Nature · doi:10.1038/nature18933 · Cited by 5,111
Self-citationMultimodal population brain imaging in the UK Biobank prospective epidemiological study
Miller, K. L., Alfaro-Almagro, F., Bangerter, N. K., Thomas, D. L., Yacoub, E., Xu, J., Bartsch, A. J., Jbabdi, S., Sotiropoulos, S. N., Andersson, J. L. R., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4393 · Cited by 2,020
Self-citationIntrinsic and task-evoked network architectures of the human brain
Cole, M. W., Bassett, D. S., Power, J. D., Braver, T. S., & Petersen, S. E. (2014) · Neuron · doi:10.1016/j.neuron.2014.05.014 · Cited by 1,564
Using connectome-based predictive modeling to predict individual behavior from brain connectivity
Shen, X.-L., Finn, E., Scheinost, D., Rosenberg, M., Chun, M. M., Papademetris, X., & Constable, R. T. (2017) · Nature Protocols · doi:10.1038/nprot.2016.178 · Cited by 1,088
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Metadata
- Authors
- Smith, S. M., Vidaurre, D., Beckmann, C. F., Glasser, M. F., Jenkinson, M., Miller, K. L., Nichols, T. E., Robinson, E. C., Salimi-Khorshidi, G., Woolrich, M. W., Barch, D. M., Uğurbil, K., & Van Essen, D. C.
- Affiliations
- University of Oxford (GB)
- Radboud University Nijmegen (NL)
- Washington University in St. Louis (US)
- University of Warwick (GB)
- Corresponding author
- Smith, Stephen M.
- ORCID
- Venue
- Trends in Cognitive Sciences
- Publisher
- Elsevier BV
- Published
- 2013-12
- Volume
- 17
- Issue
- 12
- Pages
- 666-682
- ISSN
- 1364-6613 (ISSN-L)
- PMC
- PMC4004765
- OpenAlex
- W2124698428
- Semantic Scholar
- c8812e9136cba9ff05045d5d65844af68e7ceddb
- Cited by
- 952
- References
- 93
- Citations by year
- 2026: 55 · 2025: 77 · 2024: 84 · 2023: 76 · 2022: 83 · 2021: 82 · 2020: 88 · 2019: 77 · 2018: 81 · 2017: 72 · 2016: 71 · 2015: 63 · 2014: 38 · 2013: 3
- FWCI
- 4.96
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Trends in Cognitive Sciences (publishedVersion)
- PubMed (publishedVersion)
- University of Twente Research Information (publishedVersion)
- PubMed Central (acceptedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- University of Twente Research Information (submittedVersion)
- Funders
- Wellcome Trust (1U54MH091657, 098369/Z/12/Z, 098369, 100309/A/12/Z, 100309)
- National Institutes of Health (5u54mh091657-05, 1u54mh091657-01, 1U54‐MH‐091657, RR08079)
- National Institute of Mental Health (1U54-MH091657-01, U54-MH091657, F30MH097312)
- National Institute of Neurological Disorders and Stroke (P30NS076408, P30NS057091)
- National Institute of Biomedical Imaging and Bioengineering (P41EB015894, P41-RR08079/EB015894)
- National Center for Research Resources (P41RR008079)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Functional Brain Connectivity Studies
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced Neuroimaging Techniques and Applications
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Advanced MRI Techniques and Applications
- Keywords
- functional connectomics, resting-state fMRI, spontaneous brain activity, functional brain networks, network structure estimation, Human Connectome Project, MRI image processing, connectome mapping
- MeSH terms
- Animals, Brain, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Nerve Net, Neural Pathways, Oxygen, Rest
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-09, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-09 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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