Visualizations of input volume mapped with output segmentation labels
Visualization of segmented organs only
Useful transfer function from itkwidget, supports slice view
Implementations are in the ./UNETR/BCTV
folder
- Inside the folder, follow instructions to install dependencies of UNETR.
- Then, download pretrained models (link provided) and put into
./pretrained_models
folder - For repository's space sake, I've uploaded 1 abdominal CT scan volume with corresponding label. Check
./dataset
folder
pip install notebook
pip install itkwidgets
To see results, simply run the ./test.ipynb
file.
UNETR: https://github.com/Project-MONAI/research-contributions/tree/master/UNETR/BTCV
itkwidget: https://github.com/InsightSoftwareConsortium/itkwidgets