xnatcli 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.
Full documentation for every xnatcli subcommand, the on-disk layouts each one produces, and how the pieces fit together lives at xnatbidscli.readthedocs.io.
uv syncSee the Installation guide for making the xnatcli command available on PATH and the full list of runtime dependencies.
Use the GitHub Issues feature here to report anything wrong with the CLI, code, or docs. You can also provide feature requests via GitHub Issues.
Developed and tested primarily by Eric Earl of the NIMH Data Science and Sharing Team 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.
Distributed under the MIT License.