bids-manager 1.0.3

Schema-driven BIDS converter, curator, and editor (re-imagination of BIDS-Manager v0.2.5)

Making raw-to-BIDS less painful.

What is BIDS Manager?

BIDS Manager is a desktop app that helps researchers turn raw MRI, EEG, and MEG recordings into BIDS-compliant datasets. It scans your raw data, lets you review and fix every conversion decision in a spreadsheet, runs the conversion, and then opens the result for metadata editing, volume inspection, and validation. All in one place, without writing scripts or editing JSON files by hand.

pip install bids-manager
bidsmgr

The workflow

Each feature below maps to one of the stages above.

Features

1. See what you have

Point the app at a folder of DICOM, EEG, or MEG recordings, or all three at once. It walks the tree, classifies every series, and shows the proposed BIDS names in a spreadsheet you can sort, filter, and bulk-edit.

2. Convert with confidence

Override any cell before you commit. Subject names, sessions, tasks, runs: everything updates the BIDS filename live. Hit Run and BIDS Manager handles dcm2niix, mne-bids, and the physio backends behind the scenes, with atomic staging so a failure never leaves your output tree half-converted.

3. Fix metadata visually

JSON sidecars become forms. Required fields appear in red, recommended in amber, and missing fields are listed for you with empty inputs ready to fill. TSVs open in an editable table. No more hand-editing files in a text editor.

4. Inspect your volumes

A built-in NIfTI viewer with single-slice and tri-view modes. Drag the crosshair across all three orientations at once. For 4D data, a time-series plot shows the signal at the crosshair voxel, with a scope grid for neighbouring voxels.

5. Validate in one click

Run the official BIDS validator against your dataset. Every error is clickable. It takes you straight to the offending file, scrolls to the broken field, and opens it for editing. Fix it, revalidate, done.

6. Provenance built in

Every action you take is recorded in your project file. Undo a mistake from yesterday. See why a subject was renamed. Your dataset arrives with its history attached in dataset_description.json, so anyone who picks it up can trace what happened and when.

Get started

pip install bids-manager   # needs Python 3.10 or newer
bidsmgr                    # launch the GUI

Prefer the command line? Five verbs cover the whole pipeline: bidsmgr-scan, bidsmgr-rebuild, bidsmgr-convert, bidsmgr-metadata, and bidsmgr-validate. See the docs for examples (docs are being updated).

Authors

Karel López Vilaret and Jochem Rieger, ANCP Lab, Carl von Ossietzky Universität Oldenburg.

License

MIT.

Physio conversion code under bidsmgr/vendor/bidsphysio/ is derived from bidsphysio by Pablo Velasco and Chrysa Papadaniil (NYU Center for Brain Imaging), used under the MIT License. See bidsmgr/vendor/bidsphysio/LICENSE and bidsmgr/vendor/README.md for the full attribution and what changed during vendoring.

Citation

López Vilaret, K. M. and Rieger, J.
BIDS Manager (v1.0.0). 2026. https://github.com/karellopez/BIDS-Manager

Documentation · Report a bug · Suggest a feature