Function run_masking 

pub fn run_masking(
    sections: &[MaskSection],
    phases: &[&[f64]],
    magnitude: Option<&[f64]>,
    metadata: &ScanMetadata,
) -> Result<Vec<u8>, PipelineError>

Build a mask from multiple sections, OR’d together.

Each section specifies an input source, a generator (threshold/BET), and optional refinements (erode, dilate, close, fill holes, smooth).

Arguments

• sections - Mask section configs
• phases - Per-echo phase arrays (for PhaseQuality input)
• magnitude - Combined magnitude (for Magnitude/BET input)
• metadata - Scan metadata