Semiautomated ROI segmentation

Semiautomated ROI segmentation tool for 2D or 3D images, based on thresholding performed after drawing a custom and adjustable ROI

Semiautomated ROI segmentation

Provided test input is bSSFP MR image of phantom containing 4 stroke clots inside separate tubes

Enter input file name and directory

Enter generated segmentation file name and directory:

When ROI_thresholding = 0, can enter multiple file names as ["A","B","C"...] to create multiple ROIs at once

Set ROI thresholding:

0: include all pixels in ROI

1: include pixels above/below a specified threshold

Set threshold type:

neg: negative threshold, all pixels below threshold will be included in ROI

pos: positive threshold, all pixels above threshold will be included in ROI

Set ROI type:

circle: adjustable circle ROI

draw: draw custom ROI

Able to accept global (x) or slice-specific thresholds ([x,y,z,...])

Able to change threshold after first segmentation attempt

Able to erode first or final X slices of drawn ROI shape (enter -X for final X slices)