Repository

TranscranialFUS Documentation

TranscranialFUS is a Julia project for transcranial ultrasound focusing and passive acoustic mapping (PAM). The repository is intended to be used primarily through the scripts in scripts/, especially scripts/run_pam.jl.

The documentation is organized around the command-line workflow:

  • Getting Started covers setup, data assumptions, and first smoke runs.
  • CLI Overview explains common command syntax and runtime behavior.
  • Running PAM is the main user guide for scripts/run_pam.jl.
  • Running Focus documents the focusing scripts kept from the earlier workflow.
  • PAM CLI Parameters is generated from CLI option metadata in the package.
  • High-Level Workflow explains what happens under the hood without going into every internal function.

The code is research-oriented and assumes access to local CT data for skull-backed examples. Homogeneous water examples do not require CT data.