BIDS Manager

Making raw-to-BIDS less painful.

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BIDS Manager in action

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.

Get started

The fastest way to set things up is the one-click bootstrap installer for macOS, Linux, and Windows. It bundles a portable Python with every dependency and registers a native desktop launcher; no prior Python install required. See the install guide for a step-by-step walkthrough.

Once installed, launch the GUI with bidsmgr. Prefer the command line? Five verbs cover the whole pipeline: bidsmgr-scan, bidsmgr-rebuild, bidsmgr-convert, bidsmgr-metadata, and bidsmgr-validate. The documentation covers the full GUI walkthrough and CLI reference.

The workflow

Raw data, then Scan, Review and edit inventory, Convert, Fix metadata, Inspect volumes, Validate, then BIDS dataset

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.

See what you have

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.

Fix metadata visually

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.

Inspect your volumes

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.

Validate in one click

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.

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

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Credits

Author: Karel Lopez Vilaret, Jochem Rieger

Maintainer: ANCP Lab, University of Oldenburg

License expression

MIT
View SPDX License List

Requires

Python <3.15, >=3.10

Provides Extra

dev

Tags

BIDS DICOM EEG MEG GUI Neuroimaging

Classifiers

Report project as malware

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