BrainMask (Preclinical)

Purpose. Robust in-brain mask via thresholding + morphology (mricloud_inbrain-inspired).

Context I/O

• Reads: ImageCtr (X,Y,Z,NR), savedir

• Writes: BrainMask (X,Y,Z)

• Optional: If relCBF is present, writes MaskedCBF.png (masked mosaic).

Parameters

Key	Type / Default	Meaning
thres	float / 0.2	Threshold scale factor (mean-of-center-box × thres)
open_iter	int / 2	2D erosions per slice
close_iter	int / 2	2D dilations per slice

YAML example

modules:
  - name: BrainMask
    params:
      thres: 0.25
      open_iter: 2
      close_iter: 2