A high-resolution 7 Tesla resting-state fMRI dataset optimized for studying the subcortex.

To achieve a comprehensive understanding of spontaneous brain dynamics in humans, in vivo acquisition of intrinsic activity across both cortical and subcortical regions is necessary. Here we present advanced whole-brain, resting-state functional magnetic resonance imaging (rs-fMRI) data acquired at 7 Tesla with 1.5 mm isotropic voxel resolution. Functional images were obtained from 56 healthy adults (33 females, ages 19-39 years) in two runs of 15 min eyes-open wakeful rest. The high spatial resolution and short echo times of the multiband echo-planar imaging (EPI) protocol optimizes blood oxygen level-dependent (BOLD)-sensitivity for the subcortex while concurrent respiratory and cardiac measures enable retrospective correction of physiological noise, resulting in data that is highly suitable for researchers interested in subcortical BOLD signal. Functional timeseries were coregistered to high-resolution T1-weighted structural data (0.75 mm isotropic voxels) acquired during the same scanning session. To accommodate data reutilization, functional and structural images were formatted to the Brain Imaging Data Structure (BIDS) and preprocessed with fMRIPrep.

Using group level factor models to resolve high dimensionality in model-based sampling.

Joint modeling of decisions and neural activation poses the potential to provide significant advances in linking brain and behavior. However, methods of joint modeling have been limited by difficulties in estimation, often due to high dimensionality and simultaneous estimation challenges. In the current article, we propose a method of model estimation that draws on state-of-the-art Bayesian hierarchical modeling techniques and uses factor analysis as a means of dimensionality reduction and inference at the group level. This hierarchical factor approach can adopt any model for the individual and distill the relationships of its parameters across individuals through a factor structure. We demonstrate the significant dimensionality reduction gained by factor analysis and good parameter recovery, and illustrate a variety of factor loading constraints that can be used for different purposes and research questions, as well as three applications of the method to previously analyzed data. We conclude that this method provides a flexible and usable approach with interpretable outcomes that are primarily data-driven, in contrast to the largely hypothesis-driven methods often used in joint modeling. Although we focus on joint modeling methods, this model-based estimation approach could be used for any high dimensional modeling problem. We provide open-source code and accompanying tutorial documentation to make the method accessible to any researchers. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Joint Modelling of Latent Cognitive Mechanisms Shared Across Decision-Making Domains.

Decision-making behavior is often understood using the framework of evidence accumulation models (EAMs). Nowadays, EAMs are applied to various domains of decision-making with the underlying assumption that the latent cognitive constructs proposed by EAMs are consistent across these domains. In this study, we investigate both the extent to which the parameters of EAMs are related between four different decision-making domains and across different time points. To that end, we make use of the novel joint modelling approach, that explicitly includes relationships between parameters, such as covariances or underlying factors, in one combined joint model. Consequently, this joint model also accounts for measurement error and uncertainty within the estimation of these relations. We found that EAM parameters were consistent between time points on three of the four decision-making tasks. For our between-task analysis, we constructed a joint model with a factor analysis on the parameters of the different tasks. Our two-factor joint model indicated that information processing ability was related between the different decision-making domains. However, other cognitive constructs such as the degree of response caution and urgency were only comparable on some domains.

Modelling decision-making biases.

Biases are a fundamental aspect of everyday life decision-making. A variety of modelling approaches have been suggested to capture decision-making biases. Statistical models are a means to describe the data, but the results are usually interpreted according to a verbal theory. This can lead to an ambiguous interpretation of the data. Mathematical cognitive models of decision-making outline the structure of the decision process with formal assumptions, providing advantages in terms of prediction, simulation, and interpretability compared to statistical models. We compare studies that used both signal detection theory and evidence accumulation models as models of decision-making biases, concluding that the latter provides a more comprehensive account of the decision-making phenomena by including response time behavior. We conclude by reviewing recent studies investigating attention and expectation biases with evidence accumulation models. Previous findings, reporting an exclusive influence of attention on the speed of evidence accumulation and prior probability on starting point, are challenged by novel results suggesting an additional effect of attention on non-decision time and prior probability on drift rate.

Echoes from Intrinsic Connectivity Networks in the Subcortex.

Decades of research have greatly improved our understanding of intrinsic human brain organization in terms of functional networks and the transmodal hubs within the cortex at which they converge. However, substrates of multinetwork integration in the human subcortex are relatively uncharted. Here, we leveraged recent advances in subcortical atlasing and ultra-high field (7 T) imaging optimized for the subcortex to investigate the functional architecture of 14 individual structures in healthy adult males and females with a fully data-driven approach. We revealed that spontaneous neural activity in subcortical regions can be decomposed into multiple independent subsignals that correlate with, or "echo," the activity in functional networks across the cortex. Distinct subregions of the thalamus, striatum, claustrum, and hippocampus showed a varied pattern of echoes from attention, control, visual, somatomotor, and default mode networks, demonstrating evidence for a heterogeneous organization supportive of functional integration. Multiple network activity furthermore converged within the globus pallidus externa, substantia nigra, and ventral tegmental area but was specific to one subregion, while the amygdala and pedunculopontine nucleus preferentially affiliated with a single network, showing a more homogeneous topography. Subregional connectivity of the globus pallidus interna, subthalamic nucleus, red nucleus, periaqueductal gray, and locus coeruleus did not resemble patterns of cortical network activity. Together, these finding describe potential mechanisms through which the subcortex participates in integrated and segregated information processing and shapes the spontaneous cognitive dynamics during rest.SIGNIFICANCE STATEMENT Despite the impact of subcortical dysfunction on brain health and cognition, large-scale functional mapping of subcortical structures severely lags behind that of the cortex. Recent developments in subcortical atlasing and imaging at ultra-high field provide new avenues for studying the intricate functional architecture of the human subcortex. With a fully data-driven analysis, we reveal subregional connectivity profiles of a large set of noncortical structures, including those rarely studied in fMRI research. The results have implications for understanding how the functional organization of the subcortex facilitates integrative processing through cross-network information convergence, paving the way for future work aimed at improving our knowledge of subcortical contributions to intrinsic brain dynamics and spontaneous cognition.

Mixed methodology in human brain research: integrating MRI and histology.

Postmortem magnetic resonance imaging (MRI) can provide a bridge between histological observations and the in vivo anatomy of the human brain. Approaches aimed at the co-registration of data derived from the two techniques are gaining interest. Optimal integration of the two research fields requires detailed knowledge of the tissue property requirements for individual research techniques, as well as a detailed understanding of the consequences of tissue fixation steps on the imaging quality outcomes for both MRI and histology. Here, we provide an overview of existing studies that bridge between state-of-the-art imaging modalities, and discuss the background knowledge incorporated into the design, execution and interpretation of postmortem studies. A subset of the discussed challenges transfer to animal studies as well. This insight can contribute to furthering our understanding of the normal and diseased human brain, and to facilitate discussions between researchers from the individual disciplines.

A unified model for reconstruction and R2* mapping of accelerated 7T data using the quantitative recurrent inference machine.

Quantitative MRI (qMRI) acquired at the ultra-high field of 7 Tesla has been used in visualizing and analyzing subcortical structures. qMRI relies on the acquisition of multiple images with different scan settings, leading to extended scanning times. Data redundancy and prior information from the relaxometry model can be exploited by deep learning to accelerate the imaging process. We propose the quantitative Recurrent Inference Machine (qRIM), with a unified forward model for joint reconstruction and R2*-mapping from sparse data, embedded in a Recurrent Inference Machine (RIM), an iterative inverse problem-solving network. To study the dependency of the proposed extension of the unified forward model to network architecture, we implemented and compared a quantitative End-to-End Variational Network (qE2EVN). Experiments were performed with high-resolution multi-echo gradient echo data of the brain at 7T of a cohort study covering the entire adult life span. The error in reconstructed R2* from undersampled data relative to reference data significantly decreased for the unified model compared to sequential image reconstruction and parameter fitting using the RIM. With increasing acceleration factor, an increasing reduction in the reconstruction error was observed, pointing to a larger benefit for sparser data. Qualitatively, this was following an observed reduction of image blurriness in R2*-maps. In contrast, when using the U-Net as network architecture, a negative bias in R2* in selected regions of interest was observed. Compressed Sensing rendered accurate, but less precise estimates of R2*. The qE2EVN showed slightly inferior reconstruction quality compared to the qRIM but better quality than the U-Net and Compressed Sensing. Subcortical maturation over age measured by a linearly increasing interquartile range of R2* in the striatum was preserved up to an acceleration factor of 9. With the integrated prior of the unified forward model, the proposed qRIM can exploit the redundancy among repeated measurements and shared information between tasks, facilitating relaxometry in accelerated MRI.

7T functional MRI finds no evidence for distinct functional subregions in the subthalamic nucleus during a speeded decision-making task.

The subthalamic nucleus (STN) is a small, subcortical brain structure. It is a target for deep brain stimulation, an invasive treatment that reduces motor symptoms of Parkinson's disease. Side effects of DBS are commonly explained using the tripartite model of STN organization, which proposes three functionally distinct subregions in the STN specialized in cognitive, limbic, and motor processing. However, evidence for the tripartite model exclusively comes from anatomical studies and functional studies using clinical patients. Here, we provide the first experimental tests of the tripartite model in healthy volunteers using ultra-high field 7 Tesla (T) functional magnetic resonance imaging (fMRI). Thirty-four participants performed a random-dot motion decision-making task with a difficulty manipulation and a choice payoff manipulation aimed to differentially affect cognitive and limbic networks. Moreover, participants responded with their left and right index finger, differentially affecting motor networks. We analysed BOLD signal in three subregions of the STN along the dorsolateral-ventromedial axis, identified using manually delineated high resolution anatomical images and based on a previously published atlas. Using these paradigms, all segments responded equally to the experimental manipulations, and the tasks did not provide evidence for the tripartite model.

Self-reported mind wandering reflects executive control and selective attention.

Mind wandering is ubiquitous in everyday life and has a pervasive and profound impact on task-related performance. A range of psychological processes have been proposed to underlie these performance-related decrements, including failures of executive control, volatile information processing, and shortcomings in selective attention to critical task-relevant stimuli. Despite progress in the development of such theories, existing descriptive analyses have limited capacity to discriminate between the theories. We propose a cognitive-model based analysis that simultaneously explains self-reported mind wandering and task performance. We quantitatively compare six explanations of poor performance in the presence of mind wandering. The competing theories are distinguished by whether there is an impact on executive control and, if so, how executive control acts on information processing, and whether there is an impact on volatility of information processing. Across two experiments using the sustained attention to response task, we find quantitative evidence that mind wandering is associated with two latent factors. Our strongest conclusion is that executive control is impaired: increased mind wandering is associated with reduced ability to inhibit habitual response tendencies. Our nuanced conclusion is that executive control deficits manifest in reduced ability to selectively attend to the information value of rare but task-critical events.

A high-resolution multi-shell 3T diffusion magnetic resonance imaging dataset as part of the Amsterdam Ultra-high field adult lifespan database (AHEAD).

In order to further our understanding of brain function and the underlying networks, more advanced diffusion weighted magnetic resonance imaging (DWI MRI) data are essential. Here we present freely available high-resolution multi-shell multi-directional 3 Tesla (T) DWI MRI data as part of the 'Amsterdam Ultra-high field adult lifespan database' (AHEAD). The 3T DWI AHEAD dataset include 1.28mm isotropic whole brain DWI data of 49 healthy adult participants between 18 and 90 years old. The acquired data include DWIs at three non-zero b-values (48 directions, b-value 700 s/mm2; 56 directions, b-value 1000 s/mm2; 64 directions, b-value 1600 s/mm2) including a total of twelve volumes with a b-value of 0 s/mm2 (b0 volumes). In addition, eight b0 volumes with a reversed phase encoding direction were acquired to correct for distortions. To facilitate future use, the DWI data have been denoised, corrected for eddy currents, susceptibility-induced off-resonance field distortions, bias fields, and are skull stripped.

A unified 3D map of microscopic architecture and MRI of the human brain.

We present the first three-dimensional (3D) concordance maps of cyto- and fiber architecture of the human brain, combining histology, immunohistochemistry, and 7-T quantitative magnetic resonance imaging (MRI), in two individual specimens. These 3D maps each integrate data from approximately 800 microscopy sections per brain, showing neuronal and glial cell bodies, nerve fibers, and interneuronal populations, as well as ultrahigh-field quantitative MRI, all coaligned at the 200-µm scale to the stacked blockface images obtained during sectioning. These unprecedented 3D multimodal datasets are shared without any restrictions and provide a unique resource for the joint study of cell and fiber architecture of the brain, detailed anatomical atlasing, or modeling of the microscopic underpinnings of MRI contrasts.

Charting human subcortical maturation across the adult lifespan with in vivo 7 T MRI.

The human subcortex comprises hundreds of unique structures. Subcortical functioning is crucial for behavior, and disrupted function is observed in common neurodegenerative diseases. Despite their importance, human subcortical structures continue to be difficult to study in vivo. Here we provide a detailed account of 17 prominent subcortical structures and ventricles, describing their approximate iron and myelin contents, morphometry, and their age-related changes across the normal adult lifespan. The results provide compelling insights into the heterogeneity and intricate age-related alterations of these structures. They also show that the locations of many structures shift across the lifespan, which is of direct relevance for the use of standard magnetic resonance imaging atlases. The results further our understanding of subcortical morphometry and neuroimaging properties, and of normal aging processes which ultimately can improve our understanding of neurodegeneration.

Catching wandering minds with tapping fingers: neural and behavioral insights into task-unrelated cognition.

When the human mind wanders, it engages in episodes during which attention is focused on self-generated thoughts rather than on external task demands. Although the sustained attention to response task is commonly used to examine relationships between mind wandering and executive functions, limited executive resources are required for optimal task performance. In the current study, we aimed to investigate the relationship between mind wandering and executive functions more closely by employing a recently developed finger-tapping task to monitor fluctuations in attention and executive control through task performance and periodical experience sampling during concurrent functional magnetic resonance imaging (fMRI) and pupillometry. Our results show that mind wandering was preceded by increases in finger-tapping variability, which was correlated with activity in dorsal and ventral attention networks. The entropy of random finger-tapping sequences was related to activity in frontoparietal regions associated with executive control, demonstrating the suitability of this paradigm for studying executive functioning. The neural correlates of behavioral performance, pupillary dynamics, and self-reported attentional state diverged, thus indicating a dissociation between direct and indirect markers of mind wandering. Together, the investigation of these relationships at both the behavioral and neural level provided novel insights into the identification of underlying mechanisms of mind wandering.

Manual delineation approaches for direct imaging of the subcortex.

The growing interest in the human subcortex is accompanied by an increasing number of parcellation procedures to identify deep brain structures in magnetic resonance imaging (MRI) contrasts. Manual procedures continue to form the gold standard for parcellating brain structures and is used for the validation of automated approaches. Performing manual parcellations is a tedious process which requires a systematic and reproducible approach. For this purpose, we created a series of protocols for the anatomical delineation of 21 individual subcortical structures. The intelligibility of the protocols was assessed by calculating Dice similarity coefficients for ten healthy volunteers. In addition, dilated Dice coefficients showed that manual parcellations created using these protocols can provide high-quality training data for automated algorithms. Here, we share the protocols, together with three example MRI datasets and the created manual delineations. The protocols can be applied to create high-quality training data for automated parcellation procedures, as well as for further validation of existing procedures and are shared without restrictions with the research community.

Structure-function similarities in deep brain stimulation targets cross-species.

Deep Brain Stimulation (DBS) is an effective neurosurgical treatment to alleviate motor symptoms of advanced Parkinson's disease. Due to its potential, DBS usage is rapidly expanding to target a large number of brain regions to treat a wide range of diseases and neuropsychiatric disorders. The identification and validation of new target regions heavily rely on the insights gained from rodent and primate models. Here we present a large-scale automatic meta-analysis in which the structure-function associations within and between species are compared for 21 DBS targets in humans. The results indicate that the structure-function association for the majority of the 21 included subcortical areas were conserved cross-species. A subset of structures showed overlapping functional association. This can potentially be attributed to shared brain networks and might explain why multiple brain areas are targeted for the same disease or neuropsychiatric disorder.

Variability in subthalamic nucleus targeting for deep brain stimulation with 3 and 7 Tesla magnetic resonance imaging.

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is an effective surgical treatment for Parkinson's disease (PD). Side-effects may, however, be induced when the DBS lead is placed suboptimally. Currently, lower field magnetic resonance imaging (MRI) at 1.5 or 3 Tesla (T) is used for targeting. Ultra-high-field MRI (7 T and above) can obtain superior anatomical information and might therefore be better suited for targeting. This study aims to test whether optimized 7 T imaging protocols result in less variable targeting of the STN for DBS compared to clinically utilized 3 T images. Three DBS-experienced neurosurgeons determined the optimal STN DBS target site on three repetitions of 3 T-T2, 7 T-T2*, 7 T-R2* and 7 T-QSM images for five PD patients. The distance in millimetres between the three repetitive coordinates was used as an index of targeting variability and was compared between field strength, MRI contrast and repetition with a Bayesian ANOVA. Further, the target coordinates were registered to MNI space, and anatomical coordinates were compared between field strength, MRI contrast and repetition using a Bayesian ANOVA. The results indicate that the neurosurgeons are stable in selecting the DBS target site across MRI field strength, MRI contrast and repetitions. The analysis of the coordinates in MNI space however revealed that the actual selected location of the electrode is seemingly more ventral when using the 3 T scan compared to the 7 T scans.

Imaging of the human subthalamic nucleus.

The human subthalamic nucleus (STN) is a small lens shaped iron rich nucleus, which has gained substantial interest as a target for deep brain stimulation surgery for a variety of movement disorders. The internal anatomy of the human STN has not been fully elucidated, and an intensive debate, discussing the level of overlap between putative limbic, associative, and motor zones within the STN is still ongoing. In this chapter, we have summarized anatomical information obtained using different neuroimaging modalities focusing on the anatomy of the STN. Additionally, we have highlighted a number of major challenges faced when using magnetic resonance imaging (MRI) approaches for the visualization of small iron rich deep brain structures such as the STN. In vivo MRI and postmortem microscopy efforts provide valuable complementary information on the internal structure of the STN, although the results are not always fully aligned. Finally, we provide an outlook on future efforts that could contribute to the development of an integrative research approach that will help with the reconciliation of seemingly divergent results across research approaches.

Cognitive Control of Working Memory: A Model-Based Approach.

Working memory (WM)-based decision making depends on a number of cognitive control processes that control the flow of information into and out of WM and ensure that only relevant information is held active in WM's limited-capacity store. Although necessary for successful decision making, recent work has shown that these control processes impose performance costs on both the speed and accuracy of WM-based decisions. Using the reference-back task as a benchmark measure of WM control, we conducted evidence accumulation modeling to test several competing explanations for six benchmark empirical performance costs. Costs were driven by a combination of processes, running outside of the decision stage (longer non-decision time) and showing the inhibition of the prepotent response (lower drift rates) in trials requiring WM control. Individuals also set more cautious response thresholds when expecting to update WM with new information versus maintain existing information. We discuss the promise of this approach for understanding cognitive control in WM-based decision making.

A probabilistic atlas of the human ventral tegmental area (VTA) based on 7 Tesla MRI data.

Functional magnetic resonance imaging (fMRI) BOLD signal is commonly localized by using neuroanatomical atlases, which can also serve for region of interest analyses. Yet, the available MRI atlases have serious limitations when it comes to imaging subcortical structures: only 7% of the 455 subcortical nuclei are captured by current atlases. This highlights the general difficulty in mapping smaller nuclei deep in the brain, which can be addressed using ultra-high field 7 Tesla (T) MRI. The ventral tegmental area (VTA) is a subcortical structure that plays a pivotal role in reward processing, learning and memory. Despite the significant interest in this nucleus in cognitive neuroscience, there are currently no available, anatomically precise VTA atlases derived from 7 T MRI data that cover the full region of the VTA. Here, we first provide a protocol for multimodal VTA imaging and delineation. We then provide a data description of a probabilistic VTA atlas based on in vivo 7 T MRI data.