Automatic lobe segmentation and emphysema quantification. Input is a chest CT (.nii.gz) and outputs label maps for lobe segmentations and emphysema approximated as low attenuation volume (<-950HU). The tool also provides a visualization of segmentation results.
Please cite the following if you find this tool useful!
Thomas Z. Li, Ho Hin Lee, Kaiwen Xu, Riqiang Gao, Benoit M. Dawant, Fabien Maldonado, Kim L. Sandler, Bennett A. Landman. Quantifying Emphysema in Lung Screening Computed Tomography with Robust Automated Lobe Segmentation. Submitted to European Journal of Radiology on Nov. 2022.
- Download model weights from
- Populate
config.YAMLwith location of directories and model weights. Seeexample_config.YAMLfor more details. python3 -m pip install --upgrade pip \ pip install EmphysemaSeg- Running
EmphysemaSeg --config path_to_config.YAMLwill only do lobe segmentation. Add--empfor emphysema segmentation and--visfor visualization.
- This tool is designed for chest CTs with voxel dimensions in th range of 0.5-1mm x 0.5-1mm x 0.5-1.25mm (coronal x sagittal x axial).
- Segmentation of emphysema with this tool is only reliable on soft kernel CT and NOT robust to hard kernel reconstructions.
| File size | Runtime | RAM | VRAM |
|---|---|---|---|
| (512, 512, 400) | ~1m 20s | <12 GB | 6.5 GB |