https://github.com/Sikerdebaard/dcmrtstruct2nii
DICOM RT-Struct to mask
https://github.com/Sikerdebaard/dcmrtstruct2nii
Last synced: 6 months ago
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DICOM RT-Struct to mask
- Host: GitHub
- URL: https://github.com/Sikerdebaard/dcmrtstruct2nii
- Owner: Sikerdebaard
- License: mit
- Created: 2019-01-21T15:19:54.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2024-02-28T18:12:45.000Z (over 1 year ago)
- Last Synced: 2025-04-20T02:16:38.386Z (7 months ago)
- Language: Python
- Size: 4.09 MB
- Stars: 101
- Watchers: 1
- Forks: 27
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-dicom - dcmrtstruct2nii - DICOM RT-Struct to nii-mask. This is a naïve approach to rasterizing rt-struct to masks in the NIfTI format. (Libraries / Python)
README
[](https://doi.org/10.5281/zenodo.4037864)
# dcmrtstruct2nii
DICOM RT-Struct to nii-mask. This is a naïve approach to rasterizing rt-struct to masks in nii format. If there's holes in your RT-Struct then this approach will most likely not work. The RT-Struct needs to be within the bounds of the slices of the original DICOM. Rasterization is done on a slice-by-slice basis, interpolation between slices is currently unsupported.
# Interpolation
Interpolation of the mask between slices is currently unsupported. Send us an algorithm or a pull requests and we'll happly add it.
# Input file format
The DICOM and RT-Struct inputs need to be unzipped in a directory. Currently this is the only way to read the input files.
# CLI Tool
```
# install using pip and show tool help
pip install dcmrtstruct2nii
dcmrtstruct2nii --help
# list structures in DICOM RT Struct
dcmrtstruct2nii ls -r /path/to/rtstruct/file
# convert help output
dcmrtstruct2nii convert --help
# convert DICOM RT Structs to .nii.gz masks
dcmrtstruct2nii convert -r /path/to/rtstruct/file.dcm -d /path/to/original/extracted/dicom -o /output/path
```
# Python API
```
# install using pip and show tool help
pip install dcmrtstruct2nii
```
```
# lets test it
from dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs
print(list_rt_structs('/path/to/dicom/rtstruct/file.dcm'))
dcmrtstruct2nii('/path/to/dicom/rtstruct/file.dcm', '/path/to/original/extracted/dicom/files', '/output/path')
```
# License and academic use
The software is licensed [MIT License](https://github.com/Sikerdebaard/dcmrtstruct2nii/blob/master/LICENSE).
For academic use, use a presistent copy from [](https://doi.org/10.5281/zenodo.4037864).
Please cite:
```Thomas Phil, Thomas Albrecht, Skylar Gay, & Mathis Ersted Rasmussen. (2023). Sikerdebaard/dcmrtstruct2nii: dcmrtstruct2nii v5 (Version v5). Zenodo. https://doi.org/10.5281/zenodo.4037864```