Metadata-Version: 2.5
Name: xnatbidscli
Version: 2.0.0
Summary: CLI for logging into XNAT, downloading neuroimaging experiments, and converting them to BIDS.
Project-URL: Homepage, https://github.com/nimh-dsst/xnat-bids-cli
Project-URL: Documentation, https://xnatbidscli.readthedocs.io/
Project-URL: Repository, https://github.com/nimh-dsst/xnat-bids-cli
Project-URL: Issues, https://github.com/nimh-dsst/xnat-bids-cli/issues
Author-email: Eric Earl <eric.earl@nih.gov>
Maintainer-email: NIMH Data Science and Sharing Team <nimhdsst@mail.nih.gov>
License-Expression: MIT
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Python: >=3.11
Requires-Dist: bioread>=3; python_version < '3.12'
Requires-Dist: cubids>=1.2.1
Requires-Dist: dcm2bids>=3
Requires-Dist: dcm2niix>=1.0.20260416
Requires-Dist: nibabel<5.4,>=5.3; python_version < '3.12'
Requires-Dist: nibabel>=5.4.2; python_version >= '3.12'
Requires-Dist: numpy<2
Requires-Dist: pandas<2.4,>=2
Requires-Dist: phys2bids>=2.10; python_version < '3.12'
Requires-Dist: pydicom>=2.4
Requires-Dist: pyxnat>=1.6
Requires-Dist: requests>=2
Description-Content-Type: text/markdown

# XNAT CLI for BIDS

`xnatbidscli` is a command-line toolkit that takes neuroimaging data from login to analysis-ready dataset: authenticate against an XNAT (Extensible Neuroimaging Archive Toolkit) server, query and download experiments, convert them to BIDS (Brain Imaging Data Structure) with `dcm2bids`, group acquisitions with CuBIDS, map participants/sessions to anonymized IDs, and fold in physiological recordings — all through one CLI built on [PyXNAT](https://pyxnat.github.io/pyxnat/index.html).

## User Guide

Full documentation for every `xnatbidscli` subcommand, the on-disk layouts each one produces, and how the pieces fit together lives at [xnatbidscli.readthedocs.io](https://xnatbidscli.readthedocs.io/).

## Installation

Requires Python ≥ 3.11.

```bash
pip install xnatbidscli
```

See the [Installation guide](https://xnatbidscli.readthedocs.io/installation/) for installing unreleased features from source with uv and the full list of runtime dependencies.

## Reporting Issues and Feature Requests

Use the [GitHub Issues](https://github.com/nimh-dsst/xnat-bids-cli/issues) feature here to report anything wrong with the CLI, code, or docs. You can also provide feature requests via GitHub Issues.

## Attribution

Developed and tested primarily by [Eric Earl](https://github.com/ericearl) of the [NIMH Data Science and Sharing Team](https://github.com/nimh-dsst) primarily for the NIMH Intramural Research Program labs. Claude Code and GitHub Copilot were used to develop features, docs, and modifications, as prompted by Eric Earl.

## License

Distributed under the MIT License.
