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.

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.

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.

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.

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.

Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes.

The imprinted gene cluster at the telomeric end of mouse chromosome 7 contains a differentially methylated CpG island, KvDMR, that is required for the imprinting of multiple genes, including the genes encoding the maternally expressed placental-specific transcription factor ASCL2, the cyclin-dependent kinase CDKN1C, and the potassium channel KCNQ1. The KvDMR, which maps within intron 10 of Kcnq1, contains the promoter for a paternally expressed, noncoding, antisense transcript, Kcnq1ot1. A 244-base-pair deletion of the promoter on the paternal allele leads to the derepression of all silent genes tested. To distinguish between the loss of silencing as the consequence of the absence of transcription or the transcript itself, we prematurely truncated the Kcnq1ot1 transcript by inserting a transcriptional stop signal downstream of the promoter. We show that the lack of a full-length Kcnq1ot1 transcript on the paternal chromosome leads to the expression of genes that are normally paternally repressed. Finally, we demonstrate that five highly conserved repeats residing at the 5' end of the Kcnq1ot1 transcript are not required for imprinting at this locus.

A differentially methylated region within the gene Kcnq1 functions as an imprinted promoter and silencer.

The imprinted gene cluster on mouse distal chromosome 7 contains a differentially methylated CpG island that maps within the Kcnq1 gene that has been shown to be required for the imprinting of multiple genes. To evaluate models for how this imprinting control region (ICR) regulates imprinting, we have characterized it structurally and functionally. We show that the region contains a promoter for a paternally expressed anti-sense transcript, Kcnq1ot1, and we define the extent of the minimal promoter. We describe three paternal-specific nuclease hypersensitive sites immediately upstream from the start site and show that they are required for full promoter activity. The expression of Kcnq1ot1 during pre- and postnatal development is compared to that of other imprinted genes in its vicinity, Cdnkn1c and Kcnq1. The lack of coordination in their expression tends to rule out an enhancer competition model for the action of the ICR in imprinting control. Using a stable transfection assay we show that the region contains a position-independent and orientation-independent silencer. We propose, on the basis of these findings, that the Kcnq1 ICR functions as a silencer on the paternal chromosome to effect the repression of neighboring genes.