Functional ontologies for cognition: The systematic definition of structure and function

Different functions in the cingulate cortex, a meta-analytic connectivity modeling study

The cingulate cortex is a structurally heterogeneous brain region involved in emotional, cognitive and motor tasks. With the aim of identifying which behavioral domains are associated with the activation of the cingulate cortex, we performed a structure based-meta-analysis using the activation likelihood estimation (ALE), which assesses statistical significant convergence of neuroimaging studies using the BrainMap database. To map the meta-analytic coactivation maps of the cingulate cortex (MACM), we subdivided the parenchyma along the rostro-caudal axis in 12 bilateral equispaced ROIs. ROIs were not chosen according to previously suggested subdivisions, as to obtain a completely data-driven result. Studies were included with one or more activation coordinates in at least one of the 12 pre-defined ROIs. The meta-analytic connectivity profile and behavioral domains profiles were identified for each ROI. Cluster analysis was then performed on the MACM and behavioral domains to group together ROIs with similar profiles. The results showed that the cingulate cortex can be divided in three clusters according to the MACM parcellation and in four according to the behavioral domain-based parcellation. In addition, a behavioral-domain based meta-analysis was conducted and the spatial consistency of functional connectivity patterns across different domain-related ALE results was evaluated by computing probabilistic maps. These maps identified some portions of the cingulate cortex as involved in several tasks. Our results showed the existence of a more specific functional characterization of some portions of the cingulate cortex but also a great multifunctionality of others. By analyzing a large number of studies, structure based meta-analysis can greatly contribute to new insights in the functional significance of brain activations and in the role of specific brain areas in behavior.

It's about Time

The purpose of this review/opinion paper is to argue that human cognitive neuroscience has focused too little attention on how the brain may use time and time-based coding schemes to represent, process, and transfer information within and across brain regions. Instead, the majority of cognitive neuroscience studies rest on the assumption of functional localization. Although the functional localization approach has brought us a long way toward a basic characterization of brain functional organization, there are methodological and theoretical limitations of this approach. Further advances in our understanding of neurocognitive function may come from examining how the brain performs computations and forms transient functional neural networks using the rich multi-dimensional information available in time. This approach rests on the assumption that information is coded precisely in time but distributed in space; therefore, measures of rapid neuroelectrophysiological dynamics may provide insights into brain function that cannot be revealed using localization-based approaches and assumptions. Space is not an irrelevant dimension for brain organization; rather, a more complete understanding of how brain dynamics lead to behavior dynamics must incorporate how the brain uses time-based coding and processing schemes.

Reverse engineering for biologically inspired cognitive architectures: a critical analysis

Research initiatives on both sides of the Atlantic try to utilize the operational principles of organisms and brains to develop biologically inspired, artificial cognitive systems. This paper describes the standard way bio-inspiration is gained, i.e. decompositional analysis or reverse engineering. The indisputable complexity of brain and mind raise the issue of whether they can be understood by applying the standard method. Using Robert Rosen's modeling relation, the scientific analysis method itself is made a subject of discussion. It is concluded that the fundamental assumption of cognitive science, i.e. complex cognitive systems are decomposable, must be abandoned. Implications for investigations of organisms and behavior as well as for engineering artificial cognitive systems are discussed.

Predicting language outcome and recovery after stroke: the PLORAS system

The ability to comprehend and produce speech after stroke depends on whether the areas of the brain that support language have been damaged. Here, we review two different ways to predict language outcome after stroke. The first depends on understanding the neural circuits that support language. This model-based approach is a challenging endeavor because language is a complex cognitive function that involves the interaction of many different brain areas. The second approach, by contrast, does not require an understanding of why a lesion impairs language; instead, predictions are made on the basis of the recovery of previous patients with the same lesion. This approach requires a database that records the speech and language capabilities of a large population of patients who have, collectively, incurred a comprehensive range of focal brain lesions. In addition, a system is required that converts an MRI scan from a new patient into a three-dimensional description of the lesion and compares this lesion against all others on the database. The outputs of this system are the longitudinal language outcomes of corresponding patients in the database. This approach will provide the patient with a range of probable recovery patterns over a variety of language measures.

Investigating occipito-temporal contributions to reading with TMS

The debate regarding the role of ventral occipito-temporal cortex (vOTC) in visual word recognition arises, in part, from difficulty delineating the functional contributions of vOTC as separate from other areas of the reading network. Here, we investigated the feasibility of using TMS to interfere with vOTC processing in order to explore its specific contributions to visual word recognition. Three visual lexical decision experiments were conducted using neuronavigated TMS. The first demonstrated that repetitive stimulation of vOTC successfully slowed word, but not nonword, responses. The second confirmed and extended these findings by demonstrating the effect was specific to vOTC and not present in the adjacent lateral occipital complex. The final experiment used paired-pulse TMS to investigate the time course of vOTC processing for words and revealed activation starting as early as 80-120 msec poststimulus onset-significantly earlier than that expected based on electrophysiological and magnetoencephalography studies. Taken together, these results clearly indicate that TMS can be successfully used to stimulate parts of vOTC previously believed to be inaccessible and provide a new tool for systematically investigating the information processing characteristics of vOTC. In addition, the findings provide strong evidence that lexical status and frequency significantly affect vOTC processing, findings difficult to reconcile with prelexical accounts of vOTC function.

Investigating the functional heterogeneity of the default mode network using coordinate-based meta-analytic modeling

The default mode network (DMN) comprises a set of regions that exhibit ongoing, intrinsic activity in the resting state and task-related decreases in activity across a range of paradigms. However, DMN regions have also been reported as task-related increases, either independently or coactivated with other regions in the network. Cognitive subtractions and the use of low-level baseline conditions have generally masked the functional nature of these regions. Using a combination of activation likelihood estimation, which assesses statistically significant convergence of neuroimaging results, and tools distributed with the BrainMap database, we identified core regions in the DMN and examined their functional heterogeneity. Meta-analytic coactivation maps of task-related increases were independently generated for each region, which included both within-DMN and non-DMN connections. Their functional properties were assessed using behavioral domain metadata in BrainMap. These results were integrated to determine a DMN connectivity model that represents the patterns of interactions observed in task-related increases in activity across diverse tasks. Subnetwork components of this model were identified, and behavioral domain analysis of these cliques yielded discrete functional properties, demonstrating that components of the DMN are differentially specialized. Affective and perceptual cliques of the DMN were identified, as well as the cliques associated with a reduced preference for motor processing. In summary, we used advanced coordinate-based meta-analysis techniques to explicate behavior and connectivity in the default mode network; future work will involve applying this analysis strategy to other modes of brain function, such as executive function or sensorimotor systems.

Decoding the large-scale structure of brain function by classifying mental States across individuals

Brain-imaging research has largely focused on localizing patterns of activity related to specific mental processes, but recent work has shown that mental states can be identified from neuroimaging data using statistical classifiers. We investigated whether this approach could be extended to predict the mental state of an individual using a statistical classifier trained on other individuals, and whether the information gained in doing so could provide new insights into how mental processes are organized in the brain. Using a variety of classifier techniques, we achieved cross-validated classification accuracy of 80% across individuals (chance = 13%). Using a neural network classifier, we recovered a low-dimensional representation common to all the cognitive-perceptual tasks in our data set, and we used an ontology of cognitive processes to determine the cognitive concepts most related to each dimension. These results revealed a small organized set of large-scale networks that map cognitive processes across a highly diverse set of mental tasks, suggesting a novel way to characterize the neural basis of cognition.

ALE Meta-Analysis Workflows Via the Brainmap Database: Progress Towards A Probabilistic Functional Brain Atlas

With the ever-increasing number of studies in human functional brain mapping, an abundance of data has been generated that is ready to be synthesized and modeled on a large scale. The BrainMap database archives peak coordinates from published neuroimaging studies, along with the corresponding metadata that summarize the experimental design. BrainMap was designed to facilitate quantitative meta-analysis of neuroimaging results reported in the literature and supports the use of the activation likelihood estimation (ALE) method. In this paper, we present a discussion of the potential analyses that are possible using the BrainMap database and coordinate-based ALE meta-analyses, along with some examples of how these tools can be applied to create a probabilistic atlas and ontological system of describing function–structure correspondences.

Functional MRI at the crossroads

Since the observation of the blood oxygenation level dependent (BOLD) effect on measured MR signal in the brain, functional magnetic resonance imaging (fMRI) has rapidly become the tool of choice for exploring brain function in cognitive neuroscience. Although fMRI is an exciting and powerful means to examining the brain in vivo, the field has sometimes permitted itself to believe that patterns of BOLD activity reveal more than it is possible to measure given the method's spatial and temporal sampling, while concurrently not fully exploring the amount of information it provides. In this article, we examine some of the constraints on the kinds of inferences that can be supported by fMRI. We critique the concept of reverse inference that is often employed to claim some cognitive function must be present given activity in a specific region. We review the consideration of functional and effective connectivity that remain infrequently applied in cognitive neuroimaging, highlighting recent thinking on the ways in which functional imaging can be used to characterize inter-regional communication. Recent advances in neuroimaging that make it possible to assess anatomical connectivity using diffusion tensor imaging (DTI) and we discuss how these may inform interpretation of fMRI results. Descriptions of fMRI studies in the media, in some instances, serve to misrepresent fMRI's capabilities. We comment on how researchers need to faithfully represent fMRI's promise and limitations in dealing with the media. Finally, as we stand at the crossroads of fMRI research, where one pathway leads toward a rigorous understanding of cognitive operations using fMRI and another leads us to a predictable collection of observations absent of clear insight, we offer our impressions of a fruitful path for future functional imaging research.

The Future of Psychology: Connecting Mind to Brain

Psychological states such as thoughts and feelings are real. Brain states are real. The problem is that the two are not real in the same way, creating the mind-brain correspondence problem. In this article, I present a possible solution to this problem that involves two suggestions. First, complex psychological states such as emotion and cognition can be thought of as constructed events that can be causally reduced to a set of more basic, psychologically primitive ingredients that are more clearly respected by the brain. Second, complex psychological categories like emotion and cognition are the phenomena that require explanation in psychology, and, therefore, they cannot be abandoned by science. Describing the content and structure of these categories is a necessary and valuable scientific activity.

Lost in localization? The focus is meta-analysis

The recent commentary by Derrfuss J, Mar RA. (2009). Lost in localization: the need for a universal coordinate database. Neuroimage, In Press proposed a universal coordinate database to archive functional neuroimaging results. In this response, we discuss our strategy in developing the BrainMap database, which was created as a mechanism to promote coordinate-based meta-analysis methods.

Modeling Dynamic Functional Neuroimaging Data Using Structural Equation Modeling

The aims of this study were to present a method for developing a path analytic network model using data acquired from positron emission tomography. Regions of interest within the human brain were identified through quantitative activation likelihood estimation meta-analysis. Using this information, a "true" or population path model was then developed using Bayesian structural equation modeling. To evaluate the impact of sample size on parameter estimation bias, proportion of parameter replication coverage, and statistical power, a 2 group (clinical/control) × 6 (sample size: N = 10, N = 15, N = 20, N = 25, N = 50, N = 100) Markov chain Monte Carlo study was conducted. Results indicate that using a sample size of less than N = 15 per group will produce parameter estimates exhibiting bias greater than 5% and statistical power below .80.

Cultural neurolinguistics

As the only species that evolved to possess a language faculty, humans have been surprisingly generative in creating a diverse array of language systems. These systems vary in phonology, morphology, syntax, and written forms. Before the advent of modern brain-imaging techniques, little was known about how differences across languages are reflected in the brain. This chapter aims to provide an overview of an emerging area of research - cultural neurolinguistics - that examines systematic cross-cultural/crosslinguistic variations in the neural networks of languages. We first briefly describe general brain networks for written and spoken languages. We then discuss language-specific brain regions by highlighting differences in neural bases of different scripts (logographic vs. alphabetic scripts), orthographies (transparent vs. nontransparent orthographies), and tonality (tonal vs. atonal languages). We also discuss neural basis of second language and the role of native language experience in second-language acquisition. In the last section, we outline a general model that integrates culture and neural bases of language and discuss future directions of research in this area.

Selective activation around the left occipito-temporal sulcus for words relative to pictures: individual variability or false positives?

We used high‐resolution fMRI to investigate claims that learning to read results in greater left occipito‐temporal (OT) activation for written words relative to pictures of objects. In the first experiment, 9/16 subjects performing a one‐back task showed activation in ≥1 left OT voxel for words relative to pictures (P < 0.05 uncorrected). In a second experiment, another 9/15 subjects performing a semantic decision task activated ≥1 left OT voxel for words relative to pictures. However, at this low statistical threshold false positives need to be excluded. The semantic decision paradigm was therefore repeated, within subject, in two different scanners (1.5 and 3 T). Both scanners consistently localised left OT activation for words relative to fixation and pictures relative to words, but there were no consistent effects for words relative to pictures. Finally, in a third experiment, we minimised the voxel size (1.5 × 1.5 × 1.5 mm³) and demonstrated a striking concordance between the voxels activated for words and pictures, irrespective of task (naming vs. one‐back) or script (English vs. Hebrew). In summary, although we detected differential activation for words relative to pictures, these effects: (i) do not withstand statistical rigour; (ii) do not replicate within or between subjects; and (iii) are observed in voxels that also respond to pictures of objects. Our findings have implications for the role of left OT activation during reading. More generally, they show that studies using low statistical thresholds in single subject analyses should correct the statistical threshold for the number of comparisons made or replicate effects within subject. Hum Brain Mapp 2008. © 2007 Wiley‐Liss, Inc.

Cerebral Lateralization of Frontal Lobe Language Processes and Lateralization of the Posterior Visual Word Processing System

The brain areas involved in visual word processing rapidly become lateralized to the left cerebral hemisphere. It is often assumed this is because, in the vast majority of people, cortical structures underlying language production are lateralized to the left hemisphere. An alternative hypothesis, however, might be that the early stages of visual word processing are lateralized to the left hemisphere because of intrinsic hemispheric differences in processing low-level visual information as required for distinguishing fine-grained visual forms such as letters. If the alternative hypothesis was correct, we would expect posterior occipito-temporal processing stages still to be lateralized to the left hemisphere for participants with right hemisphere dominance for the frontal lobe processes involved in language production. By analyzing event-related potentials of native readers of French with either left hemisphere or right hemisphere dominance for language production (determined using a verb generation task), we were able to show that the posterior occipito-temporal areas involved in visual word processing are lateralized to the same hemisphere as language production. This finding could suggest top-down influences in the development of posterior visual word processing areas.

The neural substrates of visual perceptual learning of words: implications for the visual word form area hypothesis

Abstract It remains under debate whether the fusiform visual word form area (VWFA) is specific to visual word form and whether visual expertise increases its sensitivity (Xue et al., 2006; Cohen et al., 2002). The present study examined three related issues: (1) whether the VWFA is also involved in processing foreign writing that significantly differs from the native one, (2) the effect of visual word form training on VWFA activation after controlling the task difficulty, and (3) the transfer of visual word form learning. Eleven native English speakers were trained, during five sessions, to judge whether two subsequently flashed (100-msec duration with 200-msec interval) foreign characters (i.e., Korean Hangul) were identical or not. Visual noise was added to the stimuli to manipulate task difficulty. In functional magnetic resonance imaging scans before and after training, subjects performed the task once with the same noise level (i.e., parameter-matched scan) and once with noise level changed to match performance from pretraining to posttraining (i.e., performance-matched scan). Results indicated that training increased the accuracy in parameter-matched condition but remained constant in performance-matched condition (because of increasing task difficulty). Pretraining scans revealed stronger activation for English words than for Korean characters in the left inferior temporal gyrus and the left inferior frontal cortex, but not in the VWFA. Visual word form training significantly decreased the activation in the bilateral middle and left posterior fusiform when either parameters or performance were matched and for both trained and new items. These results confirm our conjecture that the VWFA is not dedicated to words, and visual expertise acquired with training reduces rather than increases its activity.

Object identification and lexical/semantic access in children: a functional magnetic resonance imaging study of word-picture matching

Theoretical models for lexical access to visual objects have been based mainly on adult data. To investigate the developmental aspects of object recognition and lexical access in children, a large-scale functional MRI (fMRI) study was performed in 283 normal children ages 5-18 using a word-picture matching paradigm in which children would match an aurally presented noun to one of two pictures (line drawings). Using group Independent Component Analysis (ICA), six task-related components were detected, including (a) the posterior superior temporal gyrus bilaterally; (b) the fusiform, inferior temporal, and middle occipital gyri bilaterally; (c) the dorsal aspect of the inferior frontal gyrus bilaterally, the left precuneus, the left superior/middle temporal gyrus, and the anterior cingulate; (d) the right medial fusiform gyrus; (e) a left-lateralized component including the inferior/middle frontal, middle temporal, medial frontal, and angular gyri, as well as the thalamus and the posterior cingulate; and (f) the ventral/anterior aspect of the inferior frontal gyrus bilaterally. Increased activation associated with age was seen in the components (b) and (d) (ventral visual pathway) for object recognition, and (c) and (f) likely associated with semantic maintenance and response selection. Increased activation associated with task performance was seen in components (b) and (d) (ventral visual pathway) while decreased activation associated with task performance was seen in component (f) (ventral/anterior inferior frontal gyrus). The results corroborate the continued development of the ventral visual pathway throughout the developmental period.

Notation-dependent and -independent representations of numbers in the parietal lobes

It is a commonly held view that numbers are represented in an abstract way in both parietal lobes. This view is based on failures to find differences between various notational representations. Here we show that by using relatively smaller voxels together with an adaptation paradigm and analyzing subjects on an individual basis it is possible to detect specialized numerical representations. The current results reveal a left/right asymmetry in parietal lobe function. In contrast to an abstract representation in the left parietal lobe, the numerical representation in the right parietal lobe is notation dependent and thus includes nonabstract representations. Our results challenge the commonly held belief that numbers are represented solely in an abstract way in the human brain.

Language experience shapes fusiform activation when processing a logographic artificial language: An fMRI training study

The significant role of the left midfusiform cortex in reading found in recent neuroimaging studies has led to the visual word form area (VWFA) hypothesis. This hypothesis suggests that years of experience reading native language change the visual expertise of this region to be especially sensitive to the visual form of native language. The present study aimed at testing this hypothesis by exploring the role of language experience in shaping the fusiform activation. We designed a logographic artificial language (LAL) using the visual form and pronunciation of Korean Hangul characters (but their correspondence was shuffled) and assigning arbitrary meanings to these characters. Twelve native Chinese Mandarin speakers (6 male and 6 female, 18 to 21 years old) with no prior knowledge of Korean language were trained in the visual form of these characters for 2 weeks, followed by 2 weeks each of phonological and semantic training. Behavioral data indicated that training was effective in increasing the efficiency of visual form processing and establishing the connections among visual form, sounds, and meanings. Imaging data indicated that at the pre-training stage, subjects showed stronger activation in the fusiform regions for LAL than for Chinese across both one-back visual matching task and the passive viewing task. Visual form training significantly decreased the activation of bilateral fusiform cortex and the left inferior occipital cortex, whereas phonological training increased activation in these regions, and the right fusiform remained more active after semantic training. Increased activations after phonological and semantic training were also evident in other regions involved in language processing. These findings thus do not seem to be consistent with the visual-expertise-induced-sensitivity hypothesis about fusiform regions. Instead, our results suggest that visual familiarity, phonological processing, and semantic processing all make significant but different contributions to shaping the fusiform activation.

Convergence, degeneracy and control

Understanding the neural representation and control of language in normal bilingual speakers provides insights into the factors that constrain the acquisition of another language, insights into the nature of language expertise and an understanding of the brain as an adaptive system. We illustrate both functional and structural brain changes associated with acquiring other languages and discuss the value of neuroimaging data in identifying individual differences and different phenotypes. Understanding normal variety is vital too if we are to understand the consequences of brain-damage in bilingual and polyglot speakers.

The role of the posterior fusiform gyrus in reading

Studies of skilled reading [Price, C. J., & Mechelli, A. Reading and reading disturbance. Current Opinion in Neurobiology, 15, 231-238, 2005], its acquisition in children [Shaywitz, B. A., Shaywitz, S. E., Pugh, K. R., Mencl, W. E., Fulbright, R. K., Skudlarski, P., et al. Disruption of posterior brain systems for reading in children with developmental dyslexia. Biological Psychiatry, 52, 101-110, 2002; Turkeltaub, P. E., Gareau, L., Flowers, D. L., Zeffiro, T. A., & Eden, G. F. Development of neural mechanisms for reading. Nature Neuroscience, 6, 767-773, 2003], and its impairment in patients with pure alexia [Leff, A. P., Crewes, H., Plant, G. T., Scott, S. K., Kennard, C., & Wise, R. J. The functional anatomy of single word reading in patients with hemianopic and pure alexia. Brain, 124, 510-521, 2001] all highlight the importance of the left posterior fusiform cortex in visual word recognition. We used visual masked priming and functional magnetic resonance imaging to elucidate the specific functional contribution of this region to reading and found that (1) unlike words, repetition of pseudowords ("solst-solst") did not produce a neural priming effect in this region, (2) orthographically related words such as "corner-corn" did produce a neural priming effect, but (3) this orthographic priming effect was reduced when prime-target pairs were semantically related ("teacher-teach"). These findings conflict with the notion of stored visual word forms and instead suggest that this region acts as an interface between visual form information and higher order stimulus properties such as its associated sound and meaning. More importantly, this function is not specific to reading but is also engaged when processing any meaningful visual stimulus.

Identification of degenerate neuronal systems based on intersubject variability

Group studies implicitly assume that all subjects activate one common system to sustain a particular cognitive task. Intersubject variability is generally treated as well-behaved and uninteresting noise. However, intersubject variability might result from subjects engaging different degenerate neuronal systems that are each sufficient for task performance. This would produce a multimodal distribution of intersubject variability. We have explored this idea with the help of Gaussian Mixture Modeling and Bayesian model comparison procedures. We illustrate our approach using a crossmodal priming paradigm, in which subjects perform a semantic decision on environmental sounds or their spoken names that were preceded by a semantically congruent or incongruent picture or written name. All subjects consistently activated the superior temporal gyri bilaterally, the left fusiform gyrus and the inferior frontal sulcus. Comparing a One and Two Gaussian Mixture Model of the unexplained residuals provided very strong evidence for two groups with distinct activation patterns: 6 subjects exhibited additional activations in the superior temporal sulci bilaterally, the right superior frontal and central sulcus. 11 subjects showed increased activation in the striate and the right inferior parietal cortex. These results suggest that semantic decisions on auditory-visual compound stimuli might be accomplished by two overlapping degenerate neuronal systems.

Reading and reading disturbance

Recent functional neuroimaging studies are generating novel insights into our knowledge of skilled and disturbed reading. In neurologically normal subjects, a double dissociation in neural activation in response to reading words and pseudowords has been revealed that corresponds to that observed in the comparison of semantic and phonological tasks. In patients with acquired dyslexia, functional imaging is demonstrating re-organisation within the reading system; in developmental dyslexia, functional imaging is being used to identify the impact of rehabilitation. Together, these findings have implications for cognitive models of reading that have previously relied on input from behavioural data.