niwrap 0.9.1

Neuroimaging wrappers.

⚠️ Important Notice: This is a very early release of niwrap. We do not recommend using niwrap in 'production' at this stage unless you are willing to debug, fix, and contribute descriptors.

niwrap

🧠 Python wrappers for neuroimaging command-line tools

🚀 Quick Start

from niwrap import fsl

# Brain extraction using FSL's BET
bet_output = fsl.bet(
    infile="input_image.nii.gz",
)

📦 Installation

Install the stable version from PyPI:

pip install niwrap

Or install the development version:

pip install -r https://raw.githubusercontent.com/styx-api/niwrap-python/main/requirements_remote.txt

🧰 Supported Tools

Package	Default Version	API Coverage
AFNI	24.2.06	565/611 (92.5%)
ANTs	2.5.3	72/113 (63.7%)
Convert3D	1.1.0	4/4 (100% 🎉)
dcm2niix	1.0.20240202	1/1 (100% 🎉)
FastSurfer	2.3.3	1/1 (100% 🎉)
FreeSurfer	7.4.1	696/789 (88.2%)
FSL	6.0.4	243/311 (78.1%)
Greedy	1.0.1	1/1 (100% 🎉)
MRTrix3	3.0.4	115/121 (95.0%)
MRTrix3Tissue	5.2.8	1/1 (100% 🎉)
NiftyReg	1.4.0	7/7 (100% 🎉)
Connectome Workbench	2.1.0	203/203 (100% 🎉)

🛠 Usage Examples

Usage examples and tutorials can be found in the Styx book.

🔧 Development

All code in this package is automatically generated by Styx.

🤝 Contributing

We welcome contributions! Please see our Contribution Guide for more details.

📄 License

The niwrap Python package, including all wrapper code, is licensed under the MIT License. See the LICENSE file for more details.

⚠️ Important Notice: While niwrap provides convenient Python wrappers, it does not include or distribute the actual neuroimaging tools. Each tool wrapped by niwrap (e.g., FSL, AFNI, ANTs) is subject to its own license. Users of niwrap must ensure they comply with the licenses of the underlying tools they use. The MIT License of niwrap applies only to the wrapper code, not to the tools themselves.

🙋‍♀️ Getting Help

The Styx book aims to be a starting point for new users.

If you encounter any problems or have any questions, please open an issue on our GitHub repository.

📚 Citation

If you use NiWrap in your research, please consider citing:

@article {rupprecht2025styx,
	author = {Rupprecht, Florian JM and Kai, Jason and Shrestha, Biraj and Giavasis, Steven and Xu, Ting and Glatard, Tristan and Milham, Michael P and Kiar, Gregory},
	title = {Styx: A multi-language API Generator for Command-Line Tools},
	elocation-id = {2025.07.24.666435},
	year = {2025},
	doi = {10.1101/2025.07.24.666435},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2025/07/30/2025.07.24.666435},
	eprint = {https://www.biorxiv.org/content/early/2025/07/30/2025.07.24.666435.full.pdf},
	journal = {bioRxiv}
}