Fig. 3: Brainstem communities underlying cortical function.

The Louvain community detection algorithm was applied to determine whether brainstem nuclei can be organized into distinct communities that make specific connectivity patterns with the cortex. a, Left, for all 458 nodes (400 cortical and 58 brainstem), we correlated (Spearmanʼs r) the node’s brainstem FC profile with the weighted degree pattern shown in the inset and in Fig. 2a. The density distribution of Spearman’s r for brainstem (green) and cortical (pink) nodes is shown separately as well as together (blue) (median r = 0.97). Middle, this brainstem map (weighted degree of brainstem-to-cortex FC) is regressed out of each cortical region’s brainstem FC pattern, resulting in a matrix (400 cortical regions × 58 brainstem nuclei) of FC residuals. Right, correlation matrix representing how similarly (Spearman’s r) two brainstem nuclei are functionally connected with the cortex, above and beyond the dominant pattern of connectivity between brainstem and cortex. Brainstem nuclei are ordered according to community affiliation (community colors shown on the right), and communities are outlined within the heatmap. Brackets on the right indicate how communities are joined in coarser community detection solutions. b, Community assignments from the Louvain community detection algorithm. Coronal (posterior view), sagittal and axial perspectives of brainstem nuclei are shown. Node size is proportional to weighted degree shown in Fig. 2a. See Table 1 for a list of all brainstem nuclei organized by community affiliation. c, Cortical weighted degree patterns were calculated as the sum of a cortical region’s FC with all brainstem nuclei within a specific community and are shown for all five communities. These maps represent how each brainstem community is functionally connected with the cortex. d, Each cortical weighted degree pattern in c was correlated with 123 cognitive and behavioral meta-analytic activation maps from Neurosynth²². Only the top 10% correlations are shown. Correlation coefficients for the full set of Neurosynth terms can be found in Supplementary Fig. 8.