Module mask 

Brain-mask thresholding and morphology.

Mask generation (otsu_threshold) plus morphological operations (erode/dilate/close/fill-holes, signal-gated erosion) and sphere masks.

Structs

ScannerMaskedPhase

Where a scanner wrote a fill value instead of a measured phase: scanner_masked_phase.

SignalErosionParams

Signal-gated erosion parameters. The default is the QSM-CI harmonization setting.

Constants

SCANNER_FILL_MIN_FRACTION

Smallest share of the volume a single exact phase value must cover to count as a scanner’s fill value in scanner_masked_phase: 5 %.

Functions

apply_mask_zero

Zero out elements where mask is 0.

create_sphere_mask

Create a binary sphere mask on a 3D volume

dilate_mask

Dilate a binary mask by expanding into neighboring voxels (6-connectivity).

erode_mask

Erode a binary mask by removing boundary voxels (6-connectivity).

fill_holes

Fill holes in a binary mask

morphological_close

Morphological closing (dilation followed by erosion) with a spherical structuring element of radius voxels.

otsu_threshold

Otsu’s method for automatic threshold selection

scanner_masked_phase

Find the voxels where the scanner wrote no phase: a constant fill value, the same in every echo, covering a large part of the volume.

signal_gated_erosion

Erode mask only where the signal is low (see the module docs).