Semiautomated ROI segmentation
Version 1.0.2 (8.43 MB) by
Spencer D. Christiansen
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)
Cite As
Spencer D. Christiansen (2024). Semiautomated ROI segmentation (https://www.mathworks.com/matlabcentral/fileexchange/100656-semiautomated-roi-segmentation), MATLAB Central File Exchange. Retrieved .
MATLAB Release Compatibility
Created with
R2020b
Compatible with R2018b and later releases
Platform Compatibility
Windows macOS LinuxTags
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