MRI Tools

A collection of medical image processing tools for MRI segmentation — cropping, mask hole filling, and penumbra analysis.

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📁 Tools

#	Tool	Description	Key Libraries
1	MRI Cropping Tool	GUI-based and coordinate-based cropping of high-resolution MRI images (.tif, .tiff, .jp2)	OpenCV, tifffile, glymur, NumPy
2	Mask Hole Filling	Post-processing tool for NIfTI segmentation masks — fills diagonal disconnections and buffers thin regions	NiBabel, NumPy, SciPy, scikit-image
3	Penumbra Analysis Pipeline	5-step pipeline for ischemic stroke penumbra analysis — SWI registration, infarct core segmentation, hypoperfused region detection, penumbra computation, and 3D outline generation	NiBabel, NumPy, SciPy, SimpleITK

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🗂️ Repository Structure

mri-tools/
├── cropping-tool/
│   ├── crop.py
│   ├── brain_downsampled.tif
│   ├── autocrop_brain_downsampled.tif
│   └── README.md
├── hole-filling/
│   ├── hole_fill.py
│   ├── image.png
│   └── README.md
├── penumbra-analysis/
│   ├── reg.py
│   ├── core.py
│   ├── hypoperfused.py
│   ├── penumbra.py
│   ├── penumbra_outline.py
│   ├── penumbra_outline.png
│   └── README.md
└── README.md

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🛠️ Tech Stack

• Python
• NiBabel — NIfTI file I/O
• SimpleITK — image registration
• OpenCV — GUI display and mouse interaction
• SciPy — morphological operations, connected components
• tifffile / glymur — TIFF and JPEG2000 support
• NumPy — array operations

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