pybids
bids: interface with datasets conforming to BIDS
Decision gist · record as of 2026-08-14
Yes. PyBIDS is actively maintained, has no known vulnerabilities, uses a permissive MIT license, and solves a concrete problem for neuroimaging researchers working with BIDS-formatted data. Low install friction makes it a safe choice. Install only if you work with BIDS datasets; it is not a general-purpose tool.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires Python 3.10 or later; Windows is not officially supported though most functionality may work.
- Low install friction with a pure-Python wheel and active maintenance.
- Last release was 155 days ago with an active repository (263 stars, last commit 2026-08-04).
License · maintenance · safety
permissive license (permissive) — MIT License (permissive) permits commercial and private use, modification, and distribution with minimal restrictions—only requiring attribution and inclusion of the license notice.
last release 2026-03-12 (155 days) · last repo commit 2026-08-04 · 263 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 136,311 downloads/mo, #11,399 on PyPI
Alternatives
Verify before relying
pip install pybids
from bids import BIDSLayout
layout = BIDSLayout('/path/to/bids/dataset')
subjects = layout.get_subjects()- Whether all 12 runtime dependencies are always required or only for specific modules.
- Performance characteristics when working with very large BIDS datasets.
- Current state of Windows compatibility despite official non-support claim.
What it is and what it does
PyBIDS is a Python library that centralizes interactions with brain imaging datasets formatted according to the BIDS standard. It provides tools to query, validate, and programmatically access neuroimaging data organized in the standardized BIDS layout, eliminating the need to manually navigate directory structures and file naming conventions.
The package wraps core neuroimaging tools (numpy, scipy, nibabel, pandas) and integrates with bids-validator to ensure dataset compliance. It supports Python 3 on POSIX systems (Linux, macOS) and is actively maintained by the BIDS community. Installation brings in 12 runtime dependencies by default, though core querying functionality requires only the bids-validator package.
Use it for
- Query and retrieve specific imaging files from a BIDS dataset by subject, session, task, or modality without manual directory traversal.
- Validate that a neuroimaging dataset conforms to BIDS specification before analysis or sharing.
- Programmatically access metadata and file paths for batch processing of imaging data in research pipelines.
- Generate reports on dataset structure and contents using the reports module.
- Integrate BIDS dataset access into Python-based neuroimaging analysis workflows alongside nibabel and scipy.
Worth the install?
AI-flagged interpretation of the facts on this page. Verify before relying on it.
Yes.
PyBIDS is actively maintained, has no known vulnerabilities, uses a permissive MIT license, and solves a concrete problem for neuroimaging researchers working with BIDS-formatted data. Low install friction makes it a safe choice. Install only if you work with BIDS datasets; it is not a general-purpose tool.
Install
pybids on PyPI
Before you install
Low install friction with a pure-Python wheel and active maintenance. Last release was 155 days ago with an active repository (263 stars, last commit 2026-08-04). Requires Python 3.10 or later.
Requires Python 3.10 or later; Windows is not officially supported though most functionality may work.
License in practice
MIT License (permissive) permits commercial and private use, modification, and distribution with minimal restrictions—only requiring attribution and inclusion of the license notice.
Quickstart
pip install pybids
from bids import BIDSLayout
layout = BIDSLayout('/path/to/bids/dataset')
subjects = layout.get_subjects()Verify before relying
- Whether all 12 runtime dependencies are always required or only for specific modules.
- Performance characteristics when working with very large BIDS datasets.
- Current state of Windows compatibility despite official non-support claim.
Package facts
| License | permissive license permissive |
| Python support | Supports the current Python release >=3.10 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 12 packagesnumpyscipynibabelpandasformulaicsqlalchemybids-validatorbidsschematoolsnum2wordsclickuniversal_pathlibfrozendict |
| Maintenance | Actively maintained 155 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 136,311 / month, #11,399 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 3 - AlphaEnvironment :: ConsoleIntended Audience :: Science/ResearchLicense :: OSI Approved :: MIT LicenseOperating System :: OS IndependentProgramming Language :: PythonProgramming Language :: Python :: 3Topic :: Scientific/Engineering |
Evidence: pybids-0.22.0-py3-none-any.whl
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See also bids-validator · bidsschematools · nilearn · pyxnat · mne-bids · dipy · nibabel · nipype · dicom2nifti · dicomweb-client