Start

First launch

What BIDS Manager's graphical user interface (GUI) shows when it opens, how to move between its three views, and the settings worth setting before you start.

Open BIDS Manager

With an installer, open BIDS-Manager from your applications, as Install describes for each system. With pip, uv or conda, activate the environment and run:

Terminal
bidsmgr

bidsmgr --project /path/to/dataset opens straight into a project, and bidsmgr --theme light starts in another theme.

The GUI

The first time, BIDS Manager opens on Home. Hover the numbers to see each part.

BIDS Manager's GUI on first launch, showing the Home view: a card to create a dataset, a card to open one, links to get started with a menu of sample datasets, What's new, and the list of recent projects.BIDS Manager's GUI on first launch, showing the Home view: a card to create a dataset, a card to open one, links to get started with a menu of sample datasets, What's new, and the list of recent projects.

The GUI on first launch, on Home.

  1. The header: the views, the project, Settings and the theme
  2. Home, Converter and Editor
  3. Create a new dataset
  4. Open an existing dataset
  5. Download a sample dataset
  6. What's new: this release, and the update notes
  7. Recent projects
  8. Settings
  9. Theme
  10. The status bar: messages, the version, Check updates

The header runs across the top in every view. From left to right: the logo (click it for About: the version, the lab, the authors and the acknowledgements), the three views, and, once a project is open, the project switcher. At the right are Settings (the gear) and the theme menu (the sun or the moon).

The status bar at the bottom says what BIDS Manager is doing, and holds the version number and Check updates.

The three views

View What it is for
Home Create a dataset, open one, reopen a recent project. Links to the documentation, a menu of sample datasets (for the course, take the multimodal sample from Sample data), and What's new: the announcement this release showed when it first opened, and the update notes.
Converter Scan raw data, curate the scan table of what was found, set the metadata no file records, and convert.
Editor Validate the converted dataset, edit its sidecars and tables, change its shape, view every file and check the image quality.

The Converter and the Editor work on a project: a BIDS dataset folder that BIDS Manager keeps a history in. Until one is open, the Converter says so and its controls are off. Projects creates the first one.

Once a project is open, its name appears in the header. Click it to switch to a recent project.

The header of the GUI with a project open: the logo, the Home, Converter and Editor views, the project switcher, Settings and the theme menu.The header of the GUI with a project open: the logo, the Home, Converter and Editor views, the project switcher, Settings and the theme menu.

The header, with a project open.

  1. The logo: opens About
  2. The three views
  3. The project switcher
  4. Settings
  5. The theme menu

Choose a theme

The theme menu, opened from the sun or moon button in the header: the themes in groups, each with its colours, and the current one ticked.The theme menu, opened from the sun or moon button in the header: the themes in groups, each with its colours, and the current one ticked.

The theme menu.

Click the sun or the moon at the right of the header. The menu lists every theme in four groups, each with a swatch of its colours, and marks the current one. The choice applies at once and is remembered.

Settings > Display offers the same list, and the changes you can make to any theme.

The figures on this site show Dark and Light, and follow the theme of this site: switch it with the button at the top right of this page.

Neutral

  • Graphite Neutral dark grey with no colour cast.
  • Carbon Neutral near-black on a black canvas.
  • Ash A lighter neutral charcoal.
  • Porcelain White cards on a pale grey canvas, no tint.

Classic

  • Dark Near-black with a blue cast.
  • Dim A softer blue-grey dark for long sessions.
  • Original dark The first dark theme, as it was before the restyle.
  • Light White cards on a cool grey canvas.
  • Paper Cream cards on a warm sand canvas.
  • Original light The first light theme: a white canvas with pale grey cards.

Colour

  • Nord Cool blue-grey with frost accents.
  • Ember Warm charcoal with an amber accent.
  • Forest Deep green-grey with a golden accent.
  • Aubergine Deep plum with an orchid accent.
  • Monokai The classic editor palette on warm olive-black.
  • Sakura Blush cards with a plum accent.
  • Sage Pale green-grey with a slate-blue accent.

High contrast

  • High contrast dark Black and white with strong borders.
  • High contrast light White and black with strong borders.

Settings

Click the gear in the header. The pages are listed down the left; every change applies when you click Save, and Restore Defaults puts back what BIDS Manager starts with. Each page is described in Settings.

Settings, Display page: the theme, its appearance (accent, tint, icons, file colours), the font scale, the Log, the header logo, hidden files in the Editor tree and saving sidecar edits as you go.Settings, Display page: the theme, its appearance (accent, tint, icons, file colours), the font scale, the Log, the header logo, hidden files in the Editor tree and saving sidecar edits as you go.

Settings, Display page.

Two settings on the Display page are worth setting now:

  • Font scale makes all text larger or smaller, from Compact (0.85x) to Extra large (1.50x). The figures on this site are taken at Comfortable (1.15x).
  • Appearance changes the theme you chose: its accent colour, a tint of the surfaces, the colour of the icons, and the colours of each kind of file in the file trees. A colour you pick yourself is kept separately for dark and for light themes, so one choice does not make the other unreadable.

Where BIDS Manager keeps things

What Where
Your settings and recent projects macOS: ~/Library/Preferences/com.bidsmgr.bidsmgr.plist. Windows: the registry, under HKEY_CURRENT_USER\Software\bidsmgr\bidsmgr. Linux: ~/.config/bidsmgr/bidsmgr.conf.
A project's history, scan tables and logs inside the dataset, in its .bidsmgr/ folder (The project folder)
Logs of commands run outside a project ~/.bidsmgr/logs/ (on Windows, %USERPROFILE%\.bidsmgr\logs\)

Removing BIDS Manager does not remove the settings or touch your datasets.

Updates

A few seconds after it opens, BIDS Manager asks PyPI whether a newer version exists. If one does, it says so and offers What changed (the release notes on this site), Yes (close, update and reopen) and No. Nothing about your data is sent. Check updates in the status bar asks again at any time.

The check is skipped when BIDS Manager runs from a source checkout. To turn it off everywhere, for example on a computer without internet access, set the environment variable BIDSMGR_NO_UPDATE_CHECK=1.

Next

Download a sample dataset from Sample data, then follow the Quick start, or begin the course with BIDS in ten minutes.