Clustering of fMRI data: the elusive optimal number of clusters

Model-free methods are widely used for the processing of brain fMRI data collected under natural stimulations, sleep, or rest. Among them is the popular fuzzy c-mean algorithm, commonly combined with cluster validity (CV) indices to identify the ‘true’ number of clusters (components), in an unsupervised way. CV indices may however reveal different optimal c-partitions for the same fMRI data, and their effectiveness can be hindered by the high data dimensionality, the limited signal-to-noise ratio, the small proportion of relevant voxels, and the presence of artefacts or outliers. Here, the author investigated the behaviour of seven robust CV indices. A new CV index that incorporates both compactness and separation measures is also introduced. Using both artificial and real fMRI data, the findings highlight the importance of looking at the behavior of different compactness and separation measures, defined here as building blocks of CV indices, to depict a full description of the data structure, in particular when no agreement is found between CV indices. Overall, for fMRI, it makes sense to relax the assumption that only one unique c-partition exists, and appreciate that different c-partitions (with different optimal numbers of clusters) can be useful explanations of the data, given the hierarchical organization of many brain networks

There is no easy fix to peer review but paying referees and regulating the number of submissions might help [version 1; peer review: 2 approved, 1 approved with reservations]

The exponential increase in the number of submissions, further accelerated by generative AI, and the decline in the availability of experts are burdening the peer review process. This has led to high unethical desk rejection rates, a growing appeal for the publication of unreviewed preprints, and a worrying proliferation of predatory journals. The idea of monetarily compensating peer reviewers has been around for many years; maybe, it is time to take it seriously as one way to save the peer review process. Here, I argue that paying reviewers, when done in a fair and transparent way, is a viable solution. Like the case of professional language editors, part-time or full-time professional reviewers, managed by universities or for-profit companies, can be an integral part of modern peer review. Being a professional reviewer could be financially attractive to retired senior researchers and to researchers who enjoy evaluating papers but are not motivated to do so for free. Moreover, not all produced research needs to go through peer review, and thus persuading researchers to limit submissions to their most novel and useful research could also help bring submission volumes to manageable levels. Overall, this paper reckons that the problem is not the peer review process per se but rather its function within an academic ecosystem dominated by an unhealthy culture of ‘publish or perish’. Instead of reforming the peer review process, academia has to look for better science dissemination schemes that promote collaboration over competition, engagement over judgement, and research quality and sustainability over quantity

A tutorial on group effective connectivity analysis, part 2: second level analysis with PEB

This tutorial provides a worked example of using Dynamic Causal Modelling (DCM) and Parametric Empirical Bayes (PEB) to characterise inter-subject variability in neural circuitry (effective connectivity). This involves specifying a hierarchical model with two or more levels. At the first level, state space models (DCMs) are used to infer the effective connectivity that best explains a subject's neuroimaging timeseries (e.g. fMRI, MEG, EEG). Subject-specific connectivity parameters are then taken to the group level, where they are modelled using a General Linear Model (GLM) that partitions between-subject variability into designed effects and additive random effects. The ensuing (Bayesian) hierarchical model conveys both the estimated connection strengths and their uncertainty (i.e., posterior covariance) from the subject to the group level; enabling hypotheses to be tested about the commonalities and differences across subjects. This approach can also finesse parameter estimation at the subject level, by using the group-level parameters as empirical priors. We walk through this approach in detail, using data from a published fMRI experiment that characterised individual differences in hemispheric lateralization in a semantic processing task. The preliminary subject specific DCM analysis is covered in detail in a companion paper. This tutorial is accompanied by the example dataset and step-by-step instructions to reproduce the analyses

fMRI Evidence for Activation of Multiple Cortical Regions in the Primary Auditory Cortex of Deaf Subjects Users of Multichannel Cochlear Implants

To investigate the activation of the auditory cortex by fMRI, three deaf subjects users of the Ineraid cochlear implant participated in our study. Possible interference between fMRI acquisition and the implanted electrodes was controlled and safe experimental conditions were obtained. For each subject, electrical stimuli were applied on different intracochlear electrodes, in monopolar mode. Stimulation of each electrode was actually producing auditory sensations of different pitches, as demonstrated by psychophysical pitch-ranking measurements in the same subjects. Because deaf subjects did not hear scanner noise, the data were collected in ‘silent background' conditions, i.e. as a result of pure auditory sensations. Functional maps showed activation of the primary auditory cortex, predominantly in the left hemisphere. Stimulation of each different intracochlear electrode revealed different clusters of activation. After cluster grouping, at least three regions have been identified in the auditory cortex of each subject, and comparisons with previous architectonic and functional studies are proposed. However, a tonotopic organization could not be clearly identified within each region. These arguments, obtained without interference with unwanted scanner noise, plead in favor of a functional subdivision of the primary auditory cortex into multiple cortical regions in cochlear implant user

Identifying Abnormal Connectivity in Patients Using Dynamic Causal Modeling of fMRI Responses

Functional imaging studies of brain damaged patients offer a unique opportunity to understand how sensorimotor and cognitive tasks can be carried out when parts of the neural system that support normal performance are no longer available. In addition to knowing which regions a patient activates, we also need to know how these regions interact with one another, and how these inter-regional interactions deviate from normal. Dynamic causal modeling (DCM) offers the opportunity to assess task-dependent interactions within a set of regions. Here we review its use in patients when the question of interest concerns the characterization of abnormal connectivity for a given pathology. We describe the currently available implementations of DCM for fMRI responses, varying from the deterministic bilinear models with one-state equation to the stochastic non-linear models with two-state equations. We also highlight the importance of the new Bayesian model selection and averaging tools that allow different plausible models to be compared at the single subject and group level. These procedures allow inferences to be made at different levels of model selection, from features (model families) to connectivity parameters. Following a critical review of previous DCM studies that investigated abnormal connectivity we propose a systematic procedure that will ensure more flexibility and efficiency when using DCM in patients. Finally, some practical and methodological issues crucial for interpreting or generalizing DCM findings in patients are discussed

A tutorial on group effective connectivity analysis, part 1: first level analysis with DCM for fMRI

Dynamic Causal Modelling (DCM) is the predominant method for inferring effective connectivity from neuroimaging data. In the 15 years since its introduction, the neural models and statistical routines in DCM have developed in parallel, driven by the needs of researchers in cognitive and clinical neuroscience. In this tutorial, we step through an exemplar fMRI analysis in detail, reviewing the current implementation of DCM and demonstrating recent developments in group-level connectivity analysis. In the first part of the tutorial (current paper), we focus on issues specific to DCM for fMRI, unpacking the relevant theory and highlighting practical considerations. In particular, we clarify the assumptions (i.e., priors) used in DCM for fMRI and how to interpret the model parameters. This tutorial is accompanied by all the necessary data and instructions to reproduce the analyses using the SPM software. In the second part (in a companion paper), we move from subject-level to group-level modelling using the Parametric Empirical Bayes framework, and illustrate how to test for commonalities and differences in effective connectivity across subjects, based on imaging data from any modality

Age Affects How Task Difficulty and Complexity Modulate Perceptual Decision-Making

Decisions differ in difficulty and rely on perceptual information that varies in richness (complexity); aging affects cognitive function including decision-making, and yet, the interaction between difficulty and perceptual complexity have rarely been addressed in aging. Using a parametric fMRI modulation analysis and psychophysics, we address how task difficulty affects decision-making when controlling for the complexity of the perceptual context in which decisions are made. Perceptual complexity was varied in a factorial design while participants made perceptual judgments on the spatial frequency of two patches that either shared the same orientation (simple condition) or were orthogonal in orientation (complex condition). Psychophysical thresholds were measured for each participant in each condition and served to set individualized levels of difficulty during scanning. Findings indicate that discriminability interacts with complexity, to influence decisional difficulty. Modulation as a function of difficulty is maintained with age, as indicated by coupling between increased activation in fronto-parietal regions and suppression in the lateral hubs, however, age has a specific effect in the ventral anterior cingulate cortex (ACC), driven by performance at near-threshold (difficult) levels for the simpler stimulus combination condition, but not the more complex one. Taken together, our findings suggest that the context of difficulty, or what is perceived as important, changes with age, and that decisions that would seem neutral to younger participants, may carry more emphasis with age

Language Control and Lexical Competition in Bilinguals: An Event-Related fMRI Study

Language selection (or control) refers to the cognitive mechanism that controls which language to use at a given moment and context. It allows bilinguals to selectively communicate in one target language while minimizing the interferences from the nontarget language. Previous studies have suggested the participation in language control of different brain areas. However, the question remains whether the selection of one language among others relies on a language-specific neural module or general executive regions that also allow switching between different competing behavioral responses including the switching between various linguistic registers. In this functional magnetic resonance imaging study, we investigated the neural correlates of language selection processes in German-French bilingual subjects during picture naming in different monolingual and bilingual selection contexts. We show that naming in the first language in the bilingual context (compared with monolingual contexts) increased activation in the left caudate and anterior cingulate cortex. Furthermore, the activation of these areas is even more extended when the subjects are using a second weaker language. These findings show that language control processes engaged in contexts during which both languages must remain active recruit the left caudate and the anterior cingulate cortex (ACC) in a manner that can be distinguished from areas engaged in intralanguage task switchin

Dissociating the semantic function of two neighbouring subregions in the left lateral anterior temporal lobe

AbstractWe used fMRI in 35 healthy participants to investigate how two neighbouring subregions in the lateral anterior temporal lobe (LATL) contribute to semantic matching and object naming. Four different levels of processing were considered: (A) recognition of the object concepts; (B) search for semantic associations related to object stimuli; (C) retrieval of semantic concepts of interest; and (D) retrieval of stimulus specific concepts as required for naming. During semantic association matching on picture stimuli or heard object names, we found that activation in both subregions was higher when the objects were semantically related (mug–kettle) than unrelated (car–teapot). This is consistent with both LATL subregions playing a role in (C), the successful retrieval of amodal semantic concepts. In addition, one subregion was more activated for object naming than matching semantically related objects, consistent with (D), the retrieval of a specific concept for naming. We discuss the implications of these novel findings for cognitive models of semantic processing and left anterior temporal lobe function