Described herein are methods including determining a structural effectiveness index (SEI) for a target area of a brain which accounts for the effectiveness of a Transcranial Magnetic Stimulation (TMS) pulse based on at least one neurological feature of the brain. An SEI may include an anisotropy index (AI). An AI may account for the effectiveness of a TMS pulse based at least on the local anisotropy of the target area. An SEI may include a connectivity index (CI). A CI may account for the effectiveness of a TMS pulse at a different location of the brain than a stimulated target area. Moreover, the CI can be based at least partially on white matter tract connections. The SEI of at least one area of a brain may be used in order to plan a minimum effective dose at that location based on the actual neurological structure there, e.g. the anisotropy or white matter tracts at that area.
