---
author:
- LiRI Data Stewards
- |
  <services@linguistik.uzh.ch>
authors:
- name: LiRI Data Stewards
- name: |
    <services@linguistik.uzh.ch>
date-modified: 2026-06-30
editor: visual
number-depth: 3
repo-actions:
- edit
- issue
repo-branch: main
subtitle: Minimal steps to get started
title: Brain Imaging Data Structure (BIDS)
title-block-banner: true
toc-title: Table of contents
---

BIDS is a community-driven standard for naming and organizing
neuroimaging and associated data, designed to facilitate sharing,
collaboration, and reproducibility in neuroscience research. There is
very detailed documentation in their website (see the [BIDS Getting
Started page](https://bids.neuroimaging.io/getting_started/index.html)).
BIDS has a very active community. Besides the [BIDS
specification](https://bids-specification.readthedocs.io/en/stable/#the-brain-imaging-data-structure)
there is a [BIDS
ecosystem](https://bids.neuroimaging.io/#specification-vs-ecosystem) of
associated tools (e.g., to validate you follow the specifications). Most
analysis software for neuroimaging includes features and documentation
for working with BIDS formatted data.

Note: ALL links provided in this document are to the 'official' BIDs
documentation.

Check the following documentation highlights and the
[Section 2](#sec-workflows){.quarto-xref} with a workflow for getting
started.

## BIDS documentation highlights {#bids-documentation-highlights number="1"}

### Data folder structure {#data-folder-structure number="1.1"}

Check that the hierarchical folder structure and naming conventions are
followed. Data must be arranged in a hierarchical folder structure. The
four main levels described in the [BIDS Folders
Guide](https://bids.neuroimaging.io/getting_started/folders_and_files/folders.html)
are:

``` yaml
🗀 project
 ├──🗀 subject         
     ├── 🗀 session (if applicable)
          ├── 🗀 datatype
```

### Names {#names number="1.2"}

Name the folders as described in [BIDS Folders
Guide](https://bids.neuroimaging.io/getting_started/folders_and_files/folders.html).
E.g., `sub-<participant label>`, `ses-<session label>` and `eeg` for
data type (see more data type labels in the
[Guide](https://bids.neuroimaging.io/getting_started/folders_and_files/folders.html)
)

Although the subdirectories should be named according to BIDS, the
individual data file names may be determined by the specific application
used when acquiring or processing the data.

Details about filenaming principles and specifications are provided
[here](https://bids-specification.readthedocs.io/en/stable/common-principles.html#filenames).

An example of the
[template](https://bids-specification.readthedocs.io/en/stable/modality-specific-files/electroencephalography.html)
provided by BIDS for an EEG participant's folder is the following:

``` yaml
sub-<label>/
    [ses-<label>/]
        eeg/
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_eeg.<extension>
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_eeg.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_physio.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_physio.tsv.gz
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_stim.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_stim.tsv.gz
```

### Files types {#files-types number="1.3"}

The main [file types in
BIDS](https://bids.neuroimaging.io/getting_started/folders_and_files/files.html)
are:

#### JSON metadata

`.json` metadata files with `key:value` metadata They are placed at
multiple levels. See some code examples to create .json files
[here](https://bids.neuroimaging.io/getting_started/folders_and_files/metadata/json.html)
are examples from the [bids-example
page](https://github.com/bids-standard/bids-examples/blob/master/eeg_face13).

Example of a JSON at a data set level at folder
`eeg_face13 /dataset_description.json`

``` json
{
    "Name": "faceFO",
    "License": "ODbL (https://opendatacommons.org/licenses/odbl/summary/)",
    "Authors": [
        "James A. Desjardins",
        "Sidney J. Segalowitz"
    ],
    "HowToAcknowledge": "Desjardins, J. A., & Segalowitz, S. J. (2013). Deconstructing the early visual electrocortical responses to face and house stimuli. Journal of Vision, 13(5), 22-22.",
    "Funding": [
        "NSERC funding to Sidney Segalowitz"
    ],
    "ReferencesAndLinks": [
        "http://jov.arvojournals.org/article.aspx?articleid=2121634"
    ],
    "DatasetDOI": "10.1167/13.5.22",
    "BIDSVersion": "1.1.1"
}
```

Example of a JSON at the level of subject recording:
`eeg_face13/sub-003/eeg/sub-003_task-faceFO_eeg.json`

``` json
    {
        "TaskName": "faceFO",
        "TaskDescription": "Visual presentation of oval cropped face and house images both upright and inverted. Rare left or right half oval checkerboards were presetned as targets for keypress response.",
        "InstitutionName": "Brock University",
        "InstitutionAddress": "500 Glenridge Ave, St.Catharines, Ontario",
        "EOGChannelCount": 7,
        "EMGChannelCount": 0,
        "MiscChannelCount": 128,
        "TriggerChannelCount": 0,
        "PowerLineFrequency": 60,
        "EEGPlacementScheme": "Custom equidistant 128 channel BioSemi montage established in coordination with Judith Schedden McMaster Univertisy",
        "Manufacturer": "BioSemi",
        "ManufacturersModelName": "ActiveTwo",
        "HardwareFilters": "n/a",
        "SoftwareFilters": "n/a",
        "SoftwareVersions": "NI ActiView 532-Lores",
        "CapManufacturer": "ElectroCap International",
        "CapManufacturersModelName": "10032",
        "EEGChannelCount": 0,
        "EEGReference": "common",
        "RecordingType": "continuous",
        "RecordingDuration": 2265,
        "SamplingFrequency": 512,
        "ECGChannelCount": 0
    }
```

#### Tables with metadata

Tab-separated value `.tsv`files. E.g., with electrode locations or
events. They may be accompanied by a JSON file. See [tabular
files](https://bids-specification.readthedocs.io/en/stable/common-principles.html#tabular-files)
in BIDS documentation.

#### Data files

##### Raw data files

BIDS has methods-specific format recommendations for each type of data
(fmri, eeg., meg, etc.). See for example the details about
[EEG](https://bids-specification.readthedocs.io/en/stable/modality-specific-files/electroencephalography.html#electroencephalography)
files.

##### Derivatives

Derivatives are outputs of preprocessing pipelines, they involve data
and metadata sufficient for reuse any subsequent processing or analysis.
Because processing and analysis approaches can always be developed,
derivatives are never fully specified, but BIDS-style conventions for
these files are recommended. See details in the [Tour of BIDS
Derivative](https://bids.neuroimaging.io/getting_started/folders_and_files/derivatives.html#tour-of-a-bids-derivative)
and the more advanced page in the [specification of
derivatives](https://bids-specification.readthedocs.io/en/stable/derivatives/introduction.html).

## Workflow for getting started {#sec-workflows number="2"}

BIDS can be overwhelming but *Each step counts*. BIDS cannot specify all
possible scenarios, but try as much as possible to follow the BIDS
specifications when possible or at least follow a BIDS style structuring
as much as possible

-   [ ] *Plan and document* **folder structure, folder names** and
    **filenaming convention** based on BIDS as soon as possible,
    preferably before starting data collection
    -   Start sketching how the folder tree of raw data will look
    -   Write down the naming scheme of raw data file names
    -   Think about the derivatives (e.g., preprocessing) files. This
        might change as you run preprocessing pipelines. Update your
        documentation when needed.
-   [ ] Check what **tabular metadata files (.tsv)** you need e.g.,
    electrde coordinates, events.
    -   Write a script to save the information required into .tsv format
-   [ ] What **structured metadata (.json)** files are required?
    -   Define the fields in the file in a template, as text, JSON or in
        a table.
    -   Write code to produce JSON files.
    -   Probably easier to start setting up one JSON 'data set
        description' file that will describe all data.
    -   Then move into subject / recording specific `.JSON` files.

<div>

> **Note**
>
> Contact <services@linguistik.uzh.ch> if you need help automating the
> JSON file generation or you have other questions about how to apply
> BIDS to your data.

</div>