Repository

Running Focus

The focusing scripts are retained from the earlier transcranial focusing workflow. They are useful for comparing geometric and HASA focusing corrections through water or a CT-backed skull medium.

Single Focusing Case

Default skull-backed HASA case:

julia --project=. scripts/run_focus.jl \
  --estimator=hasa \
  --medium=skull_in_water \
  --slice-index=250

Centered target at 60 mm below the transducer:

julia --project=. scripts/run_focus.jl \
  --estimator=hasa \
  --medium=skull_in_water \
  --placement=fixed_transducer \
  --slice-index=250 \
  --lateral-cm=0.0 \
  --focal-cm=6.0

Target 30 mm below the inner skull:

julia --project=. scripts/run_focus.jl \
  --estimator=hasa \
  --medium=skull_in_water \
  --placement=fixed_focus_depth \
  --slice-index=250 \
  --focal-cm=6.0 \
  --focus-depth-from-inner-skull-mm=30

Compare Estimators

julia --project=. scripts/compare_focus_estimators.jl \
  --medium=skull_in_water \
  --slice-index=250

Main Options

  • --ct-path: DICOM folder for CT-backed skull runs.
  • --slice-index: CT slice used for the 2D focusing medium.
  • --frequency-mhz: transmit frequency.
  • --focal-cm: transducer-to-focus distance for fixed-transducer placement, or transducer distance to the resolved target for fixed-depth placement.
  • --lateral-cm: lateral target offset.
  • --aperture-cm: transducer aperture width.
  • --estimator: geometric or hasa.
  • --medium: water or skull_in_water.
  • --placement: auto, fixed_transducer, or fixed_focus_depth.
  • --focus-depth-from-inner-skull-mm: target depth below the inner skull for fixed-depth placement.
  • --out-dir: override the automatically generated output directory.

scripts/run_focus.jl writes summary.json, result.jld2, and pressure.png. scripts/compare_focus_estimators.jl writes summary.json and comparison.png.