/Deep-Segmentation-Volume-Visualization

Implementations of recent research prototypes/demonstrations using MONAI.

Primary LanguageJupyter NotebookApache License 2.0Apache-2.0

Functionalities

Visualizations of input volume mapped with output segmentation labels

4

Visualization of segmented organs only

1

Useful transfer function from itkwidget, supports slice view

3

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