Module two_pass 

Two-pass artefact reduction.

Strong susceptibility sources (air–tissue interfaces, haemorrhage, implants) leave the phase unrecoverable around them, and a phase-quality mask drops those voxels — leaving holes. Filling the holes and reconstructing once puts unreliable field values back into the inversion, and the streaking that follows spreads well beyond the hole. Dropping them instead leaves nothing to report where the source actually is.

Two-pass does both and keeps the better half of each: reconstruct once on the mask with its holes intact (“reliable”), once on the mask the user configured (“filled”), then take the reliable reconstruction wherever it is defined and the filled one everywhere else.

Stewart AW, Robinson SD, O’Brien K, et al. QSMxT: Robust masking and artifact reduction for quantitative susceptibility mapping. Magn Reson Med. 2022;87(3):1289-1300. https://doi.org/10.1002/mrm.29048

The orchestration — running the two passes, caching them, naming their outputs — belongs to the consumer, since each drives the pipeline stages itself. What lives here is the part both consumers must agree on: the default reliable-mask recipe, and the combination itself.

Functions

combine_two_pass

Combine the two passes: the reliable reconstruction where it is defined, the filled one elsewhere.

default_reliable_sections

The reliable-pass mask recipe used when the consumer does not supply one.

restrict_reliable_mask

Restrict the reliable mask to the region being reconstructed.