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dcmrtstruct2nii

(★ 103)

DICOM RT-Struct to mask

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- - python-package.yml
- - __init__.py
- - __init__.py
  - convert.py
  - dcmrtstruct2nii.py
  - liststructs.py
- - __init__.py
  - contouroutofboundsexception.py
  - invalidfileformatexception.py
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- - __init__.py
  - dcmrtstruct2nii.py
- - __init__.py
  - test_dataset_bmia.py
  - test_pr37_support_for_holes_with_xor_logic.py
- __init__.py
- cite.py
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README.md
requirements.txt
setup.py
test_requirements.txt

# Installation Guide

1. Get the code

git clone https://github.com/Sikerdebaard/dcmrtstruct2nii

Downloads the entire project code from GitHub to your computer.

cd dcmrtstruct2nii

Moves into the project folder you just downloaded.

2. Official Install Script

Easy Recommended

Prerequisites

Python 3 Python is required to use pip.

pip install dcmrtstruct2nii

Installs the package published on PyPI directly — no need to clone the source.

✅ After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.

Pulled directly from this repo's README.

3. Python

Easy

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

pip install dcmrtstruct2nii

Installs the package published on PyPI directly — no need to clone the source.

✅ If it runs without errors and prints output in the terminal, it worked.

Pulled directly from this repo's README.

// repository documentation

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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4037864.svg)](https://doi.org/10.5281/zenodo.4037864)
![unit tests](https://github.com/Sikerdebaard/dcmrtstruct2nii/workflows/Unit%20Tests/badge.svg)

# 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 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4037864.svg)](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```