Advanced configuration¶

The Advanced Options dialog of the GUI controls a large set of low-level parameters (domain generation, pseudo-CT mapping, thermal modelling, …). When scripting, you do not open that dialog — every one of those parameters is a plain entry in the bb.Config dictionary, so you set it directly:

bb = launch(...)
bb.Config['TrabecularProportion'] = 0.2       # override one advanced parameter
bb.Config['ElastixOptimizer'] = 'FiniteDifferenceGradientDescent'

When to set a parameter¶

Each parameter affects one of the pipeline steps. Set it before you trigger that step. The simplest, always-correct approach is to apply all your overrides right after launch() and before Step 1:

bb = launch(t1w=..., simbnibs=..., trajectory=..., transducer="CTX_500",
            frequency_khz=500, output_path="/data/out/")

# --- advanced overrides ---
bb.Config['bExtractAirRegions'] = True
bb.Config['TrabecularProportion'] = 0.2
bb.Config['BaselineTemperature'] = 37.0
bb.Config['HomogenousMediumValues']['Perfusion'] = 500.0

# --- then run the pipeline as usual ---
bb.Widget.CalculatePlanningMask.click()
wait_until(bb.Widget.tabWidget.isEnabled, timeout_ms=900_000)
check_no_error(bb)

bb.Config already contains every key below (initialised to the default value shown, or to the value you last saved in the GUI). You only assign the ones you want to change. The HomogenousMediumValues entry is a nested dictionary — set its members individually, e.g. bb.Config['HomogenousMediumValues']['Density'] = 1010.0.

Resetting to defaults¶

By default a scripted run inherits the advanced parameters from your previous session (the same values the GUI would show), so behaviour stays consistent with what you last configured. This is the default and nothing resets on its own.

When you instead want a deterministic, known state — e.g. for regression testing — reset every advanced parameter to its default with reset_advanced_config(bb). It is opt-in: you must call it explicitly.

bb = launch(...)
reset_advanced_config(bb)                 # every advanced param -> its default
bb.Config['TrabecularProportion'] = 0.2   # then apply only the overrides you need

reset_advanced_config restores every key listed on this page (including the nested HomogenousMediumValues and the per-transducer TxOptimizedWeights) to the defaults shown, mirroring the dialog's Reset to defaults button.

Domain generation (Step 1)¶

Pseudo-CT mapping — CT / ZTE / PETRA (Step 1)¶

Adjust the slope/offset only if you have re-fitted the ZTE/PETRA → pseudo-CT relationship for your site.

Simulation & thermal¶

Homogeneous medium (verification / benchmarking)¶

Replace the segmented head with a single homogeneous medium — useful for verification and benchmarking against analytical or reference solutions.

When enabled, the medium properties come from the nested bb.Config['HomogenousMediumValues'] dictionary:

bb.Config['bForceHomogenousMedium'] = True
hm = bb.Config['HomogenousMediumValues']
hm['Density'] = 1000.0
hm['LongSoS'] = 1500.0
hm['LongAtt'] = 5.0

Output / debugging¶

External-tool roots¶

These are folder paths used by optional integrations. The operations that use them (PlanTUS, brain segmentation, calibration) are not scriptable here, but the paths are ordinary bb.Config entries.