GUI tour

A quick tour of the GUI.

A fast walk through BIDS Manager's windows and what each one does, so you can see at a glance how the app fits together.

Want to follow along on real data?

The tutorial takes you through the same workflow step by step, from creating a project to a validated dataset.

BIDS Manager opens on a Welcome screen where you create or open a dataset project, then gives you two working views: the Converter (raw → BIDS) and the Editor (read, fix, validate). Click anything on this page to take a closer look, and switch the theme in the header to see it in light or dark.

The three views

Welcome, Converter, Editor.

BIDS Manager Welcome tab: create a dataset, open an existing one, recent projects

Welcome: start or resume a project

BIDS Manager is project-first. Before you scan anything you point it at a dataset folder, and from then on every scan, every edit, and every decision is written into that project. You can quit the app mid-curation and pick up exactly where you left off, and re-running a conversion merges new data in instead of overwriting.

Create a new dataset scaffolds a fresh BIDS folder (dataset_description.json, a README, and a .bidsignore) ready to scan raw data into. The folder name becomes the dataset slug.
Open an existing dataset continues a BIDS Manager project, or adopts a dataset created elsewhere. Adopted datasets are opened read-only so you can browse and validate them without risk.
Recent projects reopen with a double-click (right-click to remove or delete); Getting started links the docs, this tutorial, and four downloadable sample datasets.

BIDS Manager Converter view: raw and output trees, filter, inspection table, properties

Converter: raw → BIDS

The Converter is where curation happens: you review every acquisition the scanner found and decide what becomes BIDS, before a single file is written. The top header carries the Scan button, the active-project switcher, Undo / Redo, the live status chips, and Run conversion; two PathBars below show the raw input folder and the project's locked BIDS output.

Raw & output trees (left): browse the input folder as it really is on disk, and preview the exact BIDS layout the conversion will produce.
Filter / structure: every series grouped by schema entity (subject / session / datatype), so you can filter the table or exclude whole groups at once.
Inspection table: the centre of gravity, one editable row per series, colour-coded by status, with Dataset metadata, Manage columns, and Bulk edit beneath it.
Properties: a schema-aware editor for the selected row that shows only valid entities and a live predicted path.

BIDS Manager Editor view: BIDS tree, sidecar form viewer, validation pane

Editor: read, fix, validate

The Editor opens the converted dataset for review and repair. Its toolbar runs validation at three scopes (single file, folder, or whole dataset), with a Strict BIDS toggle that adds the official structural pass and severity chips that summarise the current issues.

BIDS tree: the converted layout with a status dot per file, green for clean, amber for warnings, red for errors.
Centre viewer: routes by file type, a schema-aware form for JSON sidecars, an editable table for TSVs, the tri-view for NIfTI, and an interactive signal viewer for MEG / EEG / iEEG recordings.
Validation pane: the issue list by severity; click an item to jump straight to the file that triggered it.

Features in action

From raw files to a validated dataset.

Each part of the workflow, in the order you would reach for it. Click any one to take a closer look.

1. Start a project

Create a new BIDS dataset or open an existing one, then move between open projects from the header.

Create or open a dataset

Create scaffolds a fresh BIDS dataset and starts the project bundle; Open continues a project or adopts an existing dataset. From this point on the BIDS output is locked to the chosen project, so there is no second path to mis-wire.

Switch projects from the header

Project switcher dropdown in the header — The active project is shown in the header. The dropdown lists your open and recent projects so you can jump between datasets, or return to the Welcome screen to open or create another, without losing any work.

2. Scan the raw data

Point at the raw input folder and let the scanner read the metadata inside every file. Teach it your own rules when the defaults miss something.

Point at your raw data

Choose the folder that holds your recordings (DICOM directories, EDF / FIF / BrainVision files, CTF .ds folders, physio logs). The output is already locked to the project, so this one path is all you set.

Scan

The scanner walks the folder and reads metadata from inside every file (DICOM tags, EDF / FIF headers), clusters subjects, groups series, and classifies each one. The status chips (valid / warnings / error / skipped) tick up live, and non-image or unsupported series are flagged and excluded automatically.

Teach the scanner your rules

When the classifier misses a local naming convention, the Scan rules settings tab lets you add classifier hints (force a series to a datatype / suffix / task) and series exclusions (drop anything matching a name or path). Rules are schema-constrained, persisted, and the CLI reads the same file via --rules-file.

3. Curate and inspect

Review every conversion decision before anything is written. Filter, bulk-edit, set per-row properties, enrich EEG / MEG metadata, and preview the exact BIDS tree.

Colour-coded inspection

One editable row per series, showing the predicted BIDS basename, datatype, task, run, and the classifier's confidence. Rows are tinted by status, kept, skipped, non-image, or warning, so anything that needs attention stands out immediately.

Filter and structure

A schema-grouped tree of every series, by subject, session, and datatype, with tri-state checkboxes. Filter by entity to focus the table on exactly what you want to review, or untick a whole group to drop it from the conversion.

Bulk edit

Multi-select rows, then set a datatype, task, run, or any other entity on all of them in one action, instead of editing each row by hand. Ideal for relabelling a whole session or task at once.

Manage columns

Show, hide, reorder, and resize the inventory columns to suit the dataset you are curating. Each column carries a description, and your layout is remembered between sessions.

Per-row properties

Select a row and the Properties panel builds a schema-aware editor for it: only the entities valid for that datatype + suffix appear, required fields are marked, and the predicted path updates as you type. EEG / MEG rows also carry minimal recording metadata and per-row device overrides.

Dataset metadata (EEG / MEG enrichment)

Fill dataset-wide fields once and the converter writes them into every sidecar: reference, ground, hardware filters, device and cap, institution, power-line frequency, and event labels. Modality-agnostic and modality-specific fields are colour-separated, each with its BIDS-schema tooltip.

Preview the BIDS tree

The bottom dock previews the exact filesystem layout the conversion will produce, file names, folders, and sidecars, so you can confirm everything looks right before a single byte is written.

4. Convert

Run the right backend per modality, with conversion and the post-conversion chain configurable in Settings.

Run the conversion

Each row is dispatched to the right backend (dcm2niix for DICOM, mne-bids for EEG / MEG / iEEG, bidsphysio for Siemens physio). Subjects stage in a private temp tree and commit atomically; the Log dock streams every line, and re-runs merge new data in safely.

Convert & post-convert settings

Convert and post-convert settings — Configure the number of parallel workers, residual handling, Force-EDF re-encoding, and the post-conversion chain, metadata enrichment, fix-ups, and validation, laid out as an indented hierarchy you can toggle.

5. Inspect the converted data

Open the result in the Editor and look at volumes, time series, and MEG / EEG / iEEG recordings, all rendered in-app.

NIfTI viewer

A tri-view (sagittal / coronal / axial) sharing one crosshair, plus a single-pane 2-D view. Click and drag to move the crosshair and scrub through slices.

4-D time series

For BOLD and other 4-D volumes, a graph of the signal at the crosshair voxel across all volumes, alongside the slices, for a quick sanity check of the time course.

MEG / EEG / iEEG signal viewer

A metadata card first, then load the signal into an interactive viewer: pick channels, scroll and zoom, apply high-pass / low-pass / notch filters, resample, open an in-app PSD, and overlay BIDS-native events. No external tools needed.

6. Edit and validate

Fix sidecars and tables in place, then audit the dataset against the BIDS schema and jump straight to any issue.

Edit JSON sidecars

Clicking a .json sidecar opens a schema-aware form: fields are colour-coded by level (required / recommended / optional / deprecated), and you can add or delete fields, edit values, and revert or save. A Tree view shows the raw key / value structure when you need it.

Edit TSV tables

TSV files (participants.tsv, channels.tsv, events.tsv, *_scans.tsv) open in an editable table that loads on a background thread, so even very large or wide files appear instantly and never freeze the window.

Validate the dataset

Run validation at file, folder, or whole-dataset scope. Layer 1 is the schema-driven audit; the Strict BIDS toggle adds the official structural pass. Findings are listed by severity and the tree's per-file status dots update to match.

Jump to issues from the chips

The severity chips in the toolbar are clickable: open the warnings (or errors) list, then click an entry to jump straight to the offending file in the viewer, fix it, and re-validate.

7. Settings

Sensible defaults out of the box; the gear in the header opens five tabs, each configurable and capped to your hardware.

Display

System

Scan

Scan rules

User classifier hints and series exclusions, schema-constrained and persisted. The same rules the CLI reads via --rules-file.

Convert + post-convert

Convert and post-convert settings tab — Workers, residual handling, Force-EDF, and the post-conversion chain (enrichment, fix-ups, validation) as an indented hierarchy.

Walk the tutorial → Install How it works