<p>Supplementary Material:</p><p>Figure S1 Accuracy of coregistration of fMRI data to MNI space. For each subject, the outline (red) of the MNI152 T1weighted template image is overlaid on the average fMRI EPI across time-points (sagittal slice displayed), demonstrating a good overlap of the brainstem borders in each inividual. </p><p>Figure S2 CSF mask employed for physiological noise correction. The average CSF mask across subjects is displayed (upper row, red-yellow, range [0 1]) superimposed on the MNI152 T1- weighted image (also shown in the bottom row). This mask mainly contains voxels in the CSF- spaces neighboring the brainstem, including the cerebral aqueduct and the forth ventricle. Figure S3 Preliminary validation of the probabilistic Bn atlas [11] use. For each Bn, we show (y- axis) the connectivity results (i.e. Pearson’s correlation coefficient  r-value  of each seed region with other 155 target regions) obtained using the probabilistic Bn atlas label [11] as seed region versus (x-label) those obtained using the single-subject Bn label as seed region; the fit of the latter versus the former is also displayed with a dashed line. </p><p>Figure S4 Variability of the connectivity results across the population. The mean (± s.e.) coefficient of variation (divided by the square root of the number of subjects) across significant correlation values (q = 0.05 FDR corrected) of each Bn is shown (results across left and right labels are averaged before display). </p>