Decrease of CI was consistent along neuronal loss, but atrophy was not. In DL, neuronal count parallel with neuronal area (a, d, p < 0.001). In OAH (b, e) and ON (c, f), no parallel relationship between neuronal count and neuronal area (OAH: rs = 0.092, p = 0.617, ON: rs = 0.236, p = 0.200). The CI was correlated with neuronal count in DL (g) and OAH (h) with statistical significance (DL: rs = 0.465, p = 0.007, OAH: rs = 0.434, p = 0.013). This trend was shared with ON neurons without statistical significance (i) (rs = 0.328, p = 0.072). No parallel relationship between neuronal count and CI was apparent in neurons with inclusions in all regions (j, k, l). n: neuronal count, black: control patient, blue: early ALS patient, red: advanced ALS patient p: p value, rs: Spearman’s rank correlation coefficient. *: p value < 0.05, **: p value < 0.01.