Brain stimulation is increasingly recognized as an effective therapeutic intervention for many brain diseases. Distance between the scalp and brain regions is pivotal for neurostimulation planning, but its alterations in brain diseases are largely unknown. We developed an automatic pipeline to calculate scalp-toregion distance (SRD) values from T1 MR images and applied it to 1382 participants, including patients with autism spectrum disorder (ASD), Parkinson’s disease (PD), Alzheimer’s disease (AD), and cognitively normal controls (CNs). Compared with CNs, ASD patients showed widespread SRD decreases with prominent involvement of the frontal lobe, especially the orbitofrontal cortex and adjacent regions. In contrast, in AD patients, significantly increased SRD values were observed in the frontal gyrus. No significant SRD alteration was found in PD patients. The automatic SRD calculation pipeline and the different patterns of SRD alterations in these diseases may support future validation studies for neurostimulation planning.