linliwen88 / Deep-Segmentation-Volume-Visualization

Implementations of recent research prototypes/demonstrations using MONAI.

Functionalities

Visualizations of input volume mapped with output segmentation labels

Visualization of segmented organs only

Useful transfer function from itkwidget, supports slice view

User Instuctions

Implementations are in the ./UNETR/BCTV folder

Install UNETR

1. Inside the folder, follow instructions to install dependencies of UNETR.
2. Then, download pretrained models (link provided) and put into ./pretrained_models folder
3. For repository's space sake, I've uploaded 1 abdominal CT scan volume with corresponding label. Check ./dataset folder

Install Jupyter Notebook and itkwidget

pip install notebook 
pip install itkwidgets

Run

To see results, simply run the ./test.ipynb file.

Reference

UNETR: https://github.com/Project-MONAI/research-contributions/tree/master/UNETR/BTCV

itkwidget: https://github.com/InsightSoftwareConsortium/itkwidgets