Fig. 1

Method for obtaining thickness measures from high-resolution post-mortem MRI in medial temporal lobe subregions. For each anatomical location (indicated by a dot; first row), cortical thickness was measured by using semi-automated active contour segmentation in ITK-SNAP (with possible manual correction) to segment a portion of the surrounding gray matter extending ~ 5–10 mm from the dot in all directions (second and third row). Thickness at each location was measured as the diameter of the sphere overlapping the dot, fully contained in the gray matter segmentation, and having maximum possible radius (fourth row). Segmentations and fitted spheres were visually inspected for quality assurance. See supplementary Methods for details. Note that we only show three examples in this figure. For this study we performed thickness measurements for seven subregions and averaged thickness measurements over two locations for each subregion, see Additional file 1: Fig. 1. ERC = entorhinal cortex; SRLM = stratum radiatum lacunosum moleculare; PHC = parahippocampal cortex