PyBIDS is a Python library to centralize interactions with datasets conforming BIDS (Brain Imaging Data Structure) format. For more information about BIDS visit http://bids.neuroimaging.io.
PyBIDS currently supports Python 2 and 3 on POSIX operating systems (including Mac OS). We anticipate dropping Python 2 support in the near future, and Python 2 users are encouraged to switch to Python 3. Windows is not officially supported, though most PyBIDS functionality will probably work fine.
PyBIDS is most easily installed from pip. To install the latest official release:
pip install pybids
If you want to live on the bleeding edge, you can install from master:
pip install git+https://github.com/bids-standard/pybids.git
PyBIDS has a number of dependencies. The core querying functionality requires only the BIDS-Validator package. However, most other modules require the core Python neuroimaging stack: numpy, scipy, pandas, nibabel, and patsy. The reports module additionally requires num2words. By default, all dependencies will be installed with pybids (if they aren't already available).
Get started by checking out the documentation!
Or you can start at our tutorial! You can run it interactively without installing anything via binder. Click on the link and then navigate to examples/pybids_tutorial.ipynb to explore.
Bug reports, feedback, and other contributions to PyBIDS are welcome. To report a bug, request a feature, or raise a technical (non-usage-related) question for discussion, please open an issue on GitHub. Requests for support and questions about usage (where no bug is suspected) should be posted on the NeuroStars forum. For questions about the BIDS specification or BIDS-Validator, please see the corresponding repositories. For general BIDS-related discussion, see the bids-discussion mailing list.
Pull requests are always welcome. If you have any doubts about the suitability of a PR, or want to discuss implementation-related issues, feel free to open an issue for discussion.