Workflow to quantify the extent of each cortical area’s thalamic anatomical connectivity pattern using Euclidean distance (ED). (A) Schematic overview of the thresholding and ED calculation framework applied to group-averaged and individual-level human probabilistic tractography data (n=828). ED was used to measure the extent of each cortical area’s anatomical connectivity pattern within ipsilateral thalamus (see Fig. S7 for bilateral calculation). (B) Thalamic connectivity patterns for right motor area 1 (M1) and dorsolateral prefrontal cortex (DLPFC). M1 and DLPFC exhibit focal and diffuse thalamic connections, respectively. Cortical parcels were defined via Glasser et al. (45). (C) ED matrix, depicting average pairwise distances between surviving thalamic voxels for 100 thresholds. Cortical parcels with more diffuse thalamic connections exhibited higher ED values across thresholds (e.g., DLPFC). (D) Cortical EDpc1 loading map obtained by applying principal component analysis (PCA) to the ED matrix. (E) Cortical Eσσ map showing the standard deviation of ED across 100 thresholds for each cortical parcel. EDσ almost perfectly correlated with EDpc1 (rs=0.99; psa < 0.001), with p-values estimated using spatial-autocorrelation (sa) preserving surrogate brain maps (46). rs : Spearman rho. (F) Correlations between EDpc1 and EDσ were highly consistent across subjects. (G) EDpc1 loadings and ED values across cortex negatively correlated at more conservative thresholds, indicating that higher EDpc1 loadings correspond to more focal thalamic connections.

Differences in the extent of anatomical connections within the thalamus between sensory and association cortical parcels. (A) Resting-state functional connectivity networks identified by Ji et al. (48). (B) Average EDpc1 loading within each network for each subject. Barplots show the mean and standard error. (C) Sensory networks exhibited significantly higher EDpc1 loadings compared to association networks (two-sided Wilcoxon signed-rank test; *** p < 0.001). (D) Cortical myelin map calculated by averaging T1w/T2w values across subjects. (E) Cortical principal functional gradient (RSFCpc1) loading map derived from PCA on cortico-cortical resting-state functional connectivity data. Sensory cortical parcels exhibit higher T1w/T2w values and RSFCpc1 loadings compared to association cortical parcels. (F,G) Correlations between EDpc1 loadings and T1w/T2w values, as well as RSFCpc1 loadings, across the cortex. (H,I) On average, a moderate relationship was observed between EDpc1 loadings and T1w/T2w values, as well as RSFCpc1 loadings, across subjects. Boxplots show the median and inter-quartile ranges.

Mapping between the spatial extent of anatomical connections within the tha lamus and anatomical coupling with the anteromedial-posterolateral thalamic gradient. (A) Axial view of 28 histologically-defined thalamic nuclei from the Morel thala-mic atlas (57). (B) Anatomical connectivity matrix depicting the anatomical connectivity strength between each cortical parcel and each thalamic nucleus. The y-axis is sorted such that cortical parcels with higher EDpc1 loadings are positioned near the top. (C-D) The correlation between EDpc1 loadings and Mean SC values was calculated for each thalamic nucleus for each subject. Higher values indicate thalamic nuclei that preferentially couple with cortical parcels with focal thalamic connections. (C) Posterior thalamic nuclei preferentially coupled with cortical parcels with focal thalamic connections, relative to lateral, anterior, and medial nuclei (Friedman test; *** p=0.001 for Nemenyi post-hoc tests). Each dot represents a subject’s averaged rs value across nuclei within the subclass. (D) First-order thalamic nuclei preferentially coupled with cortical parcels with focal thalamic connections (two-sided Wilcoxon signed-rank test). (E) The overlap between each cortical parcel’s anatomical connectivity along the anteromedial-posterolateral thalamic spatial gradient (P L-AMt). Positive values denote preferential coupling with anteromedial thalamus, while negative values denote preferential coupling with posterolateral thalamus (P L-AMc). (F) Cortical parcels with higher EDpc1 loadings preferen-tially coupled with the posterolateral thalamus, reflected by lower P L-AMc values.1. On average, a moderate relationship was observed between EDpc1 loadings and P L-AMc values across subjects.

Mapping between cortical variation in the extent of thalamic connectivity patterns, anatomical overlap across thalamic subpopulations, and intrinsic timescale.Thalamic gradient reflecting the relative mRNA expression of Parvalbumin (PVALB) and Calbindin (CALB1)-expressing thalamic subpopulations (CPt), which index ‘core’ and ‘matrix’ thalamic subpopulations respectively. (64). Warmer colors reflect higher CALB1 expression relative to PVALB. (B) CPt and P L-AMt values strongly correlated with one another. (C) Cortical map reflecting each cortical area’s anatomical overlap across CPt values (CPc). Warmer colors reflect preferential coupling with CALB1-expressing thalamic populations and cooler colors reflect preferential coupling with PVALB-expressing thalamic populations. (D) EDpc1 loadings and CPc values significantly correlated with one another. (E) Cortical map of z-transformed intrinsic timescale (τ), calculated from group-averaged resting-state data (65). (F) EDpc1 loadings and z-transformed τ values exhibited a trending correlation when accounting for spatial-autocorrelation.

Cortical variation of the extent of anatomical connections within the macaque thalamus. (A) Exemplar thalamic connectivity patterns for M1 (area F1; magenta) and DLPFC (area 9/46d; cyan), parcellated using the Markov Atlas (69). (B) ED matrix. (C) Cortical EDpc1 loading map. (D) Cortical myelin map, calculated by averaging T1w/T2w values across 30 macaque monkeys (70). (E) Across cortex, EDpc1 loadings positively correlated with T1w/T2w values at the group level and (F) at the subject level. (G) Cortical map reflecting anatomical coupling with the anteromedial-posterolateral thalamic spatial gradient (P L-AMt). Warmer colors reflect cortical parcels that preferentially coupled with anteromedial thalamus (P L-AMc). (H) Cortical parcels with higher EDpc1 loadings preferentially coupled with posterolateral thalamus. The red dashed line represents parcels with weak preferential coupling the P L-AMt gradient. (I) On average, EDpc1 loadings and P L-AMc value negatively correlated across monkeys.