FIG. 2.

Flowchart showing the steps of single-subject labeling of Bn (raphe magnus [RMg], in this example). For an example dataset: (a) FA map after masking out CSF areas; (b) automatic clustering of the image shown in (a) into four clusters (dark gray/white indicates, respectively, the cluster with lower/higher intensity values); (c) left panel, the cluster (dark gray) containing the RMg (white arrow) was identified; middle panel, a “disconnection-mask” (green) was manually drawn to delineate externally the shared border between the RMg and the left and right ION; right panel, labels of three-dimensional (3D) connected neighborhood components were automatically extracted (for instance, red label corresponding to the RMg, and blue/yellow labels corresponding to the left/righ ION), and within these labels, the RMg label (red) was identified by centroid matching (centroid location manually defined). In summary, the labeling procedure was automatic with some manual input, mainly provided to disconnect neighboring regions displaying similar intensity profiles, but pertaining to distinct anatomical structures. A similar procedure was applied to label the median raphe (MnR), ION, red nucleus (RN), substantia nigra (SN), subthalamic nucleus (STh), and a region comprising both the PAG and the dorsal raphe (DR), see Materials and Methods section).