https://github.com/ahmrina/unetbraintumorseg

UNetBrainTumorSeg is a 3D Slicer extension named "seg_module" that integrates a 3D UNet trained on BraTS2020 dataset to segment brain tumor area from MRI volumes
https://github.com/ahmrina/unetbraintumorseg

3d-slicer-extension monai numpy python pytorch slicer unet vtk

Last synced: 3 months ago
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UNetBrainTumorSeg is a 3D Slicer extension named "seg_module" that integrates a 3D UNet trained on BraTS2020 dataset to segment brain tumor area from MRI volumes

• Host: GitHub
• URL: https://github.com/ahmrina/unetbraintumorseg
• Owner: ahmrina
• Created: 2025-09-30T05:51:08.000Z (10 months ago)
• Default Branch: master
• Last Pushed: 2025-09-30T06:50:14.000Z (10 months ago)
• Last Synced: 2025-09-30T08:24:23.446Z (10 months ago)
• Topics: 3d-slicer-extension, monai, numpy, python, pytorch, slicer, unet, vtk
• Language: Jupyter Notebook
• Homepage:
• Size: 27.8 MB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# seg_module

UNetBrainTumorSeg is a 3D Slicer extension named "seg_module" that integrates a  3D UNet trained on BraTS2020 dataset to segment brain tumor area from MRI volumes.

## Prerequisites

3D Slicer 5.0 or later\

Python dependencies:  Pytorch, MONAI, NumPy, vtk (included with 3D Slicer)

## Module UI

![UNetBrainTumorSeg](inputs%20+ui.png)

## Segmentation example from the module

This is an example of the output after running segmentation. MRI volumes used for this example are from BraTS2020 (volumes that were *not* used for training/validation for the UNet model)

![UNetBrainTumorSeg](seg_output_example.png)

## License 

[MIT](https://choosealicense.com/licenses/mit/)