Welcome to pybids’s documentation!

pybids is a set of tools for working with Brain Imaging Data Structure (BIDS) datasets. For more information about BIDS, please visit the BIDS website.

Contents

• User guide
  • 1. Introduction: What is pybids?
  • 2. layout: Querying BIDS datasets
  • 3. analysis: Model specification for BIDS datasets
  • 4. reports: Data acquisition report generation
• Tutorials
  • Introduction to pybids
  • Writing methods reports with pybids.reports
  • Executing and inspecting StatsModels with pybids.modeling
• API Reference
  • bids.layout: Querying BIDS datasets
  • bids.modeling: Model specification for BIDS datasets
  • bids.reports: Data acquisition report generation
  • bids.variables: Variables
  • bids.config: PyBIDS Configuration utilities
  • bids.utils: Utility functions
• Changelog
  • Version 0.16.4 (November 30, 2023)
  • Version 0.16.3 (August 16, 2023)
  • Version 0.16.2 (August 11, 2023)
  • Version 0.16.1 (May 01, 2023)
  • Version 0.16.0 (April 26, 2023)
  • Version 0.15.6 (February 28, 2023)
  • Version 0.15.5 (November 07, 2022)
  • Version 0.15.4 (October 08, 2022)
  • Version 0.15.3 (September 12, 2022)
  • Version 0.15.2 (July 25, 2022)
  • Version 0.15.1 (April 04, 2022)
  • Version 0.15.0 (March 28, 2022)
  • Version 0.14.1 (March 29, 2022)
  • Version 0.14.0 (November 09, 2021)
  • Version 0.13.2 (August 20, 2021)
  • Version 0.13.1 (May 21, 2021)
  • Version 0.13 (April 14, 2021)
  • Version 0.12.4 (November 10, 2020)
  • Version 0.12.3 (October 23, 2020)
  • Version 0.12.2 (October 09, 2020)
  • Version 0.12.1 (September 09, 2020)
  • Version 0.12.0 (August 04, 2020)
  • Version 0.11.1 (July 02, 2020)
  • Version 0.11.0 (June 29, 2020)
  • Version 0.10.2 (February 26, 2020)
  • Version 0.10.1 (February 10, 2020)
  • Version 0.10.0 (December 03, 2019)
  • Version 0.9.5 (November 6, 2019)
  • Version 0.9.4 (September 20, 2019)
  • Version 0.9.3 (August 7, 2019)
  • Version 0.9.2 (July 12, 2019)
  • Version 0.9.1 (May 24, 2019)
  • Version 0.9.0 (May 21, 2019)
  • Version 0.8.0 (February 15, 2019)
  • Version 0.7.1 (February 01, 2019)
  • Version 0.7.0 (January 10, 2019)
  • Version 0.6.5 (August 21, 2018)
  • Version 0.5.1 (March 9, 2018)
  • Version 0.5.0 (March 6, 2018)
  • Version 0.4.2 (November 16, 2017)
  • Version 0.4.1 (November 3, 2017)
  • Version 0.4.0 (November 1, 2017)
  • Version 0.3.0 (August 11, 2017)
  • Version 0.2.1 (June 8, 2017)

Citing pybids

To credit PyBIDS in your work, please cite both the JOSS paper and the Zenodo archive. The former provides a high level description of the package, and the latter points to a permanent record of all PyBIDS versions (we encourage you to cite the specific version you used). Example citations (for PyBIDS 0.9.3):

Yarkoni et al., (2019). PyBIDS: Python tools for BIDS datasets. Journal of Open Source Software, 4(40), 1294, https://doi.org/10.21105/joss.01294

Yarkoni, Tal, Markiewicz, Christopher J., de la Vega, Alejandro, Gorgolewski, Krzysztof J., Halchenko, Yaroslav O., Salo, Taylor, … Blair, Ross. (2019, August 8). bids-standard/pybids: 0.9.3 (Version 0.9.3). Zenodo. https://doi.org/10.5281/zenodo.3363985

Indices and tables

• Index

• Module Index

• Search Page