The Brain Imaging Data Structure (BIDS): An Overview

The Brain Imaging Data Structure (BIDS): An Overview

Table of Contents

What is BIDS?

The Brain Imaging Data Structure (BIDS) is a community-developed standard for organizing and describing neuroimaging datasets. It provides a consistent folder structure, file naming convention, and metadata format to improve data sharing, reproducibility, and compatibility with neuroimaging software. BIDS is also a community-driven initiative providing resources and tools supporting data standardization and data sharing across multiple modalities, including community-built software and BIDS Apps.

Why Use BIDS?

Neuroimaging studies generate complex datasets that are often organized differently across research groups. Without a common standard, researchers may spend significant time understanding folder structures, renaming files, or adapting analysis scripts.

BIDS provides a consistent way to organize neuroimaging and associated behavioral data, making datasets easier to understand, share, and analyze. This standardization facilitates data aggregation and sharing large datasets across studies and institutions. For example, by making datasets consistent and interoperable, BIDS supports large-scale analyses and enables researchers to combine data from multiple projects for cross-cohort studies. BIDS also allows for linking neuroimaging data from different sources, increasing opportunities for collaboration and data reuse.

Benefits

Standardized organization
Consistent folder structure and file naming
Improved collaboration
Easier to understand and share datasets
Reproducible research
Supports consistent analysis workflows
Software compatibility
Compatible with many neuroimaging tools
Efficient data sharing
Simplifies submission to platforms such as ARCHIMEDES

How can BIDS be used?

BIDS can be incorporated throughout the research workflow, providing a standardized structure from data acquisition through data sharing and analysis.

MRI Acquisition
DICOM Images
Convert to NIfTI
Organize into BIDS
Validate Dataset
Upload to ARCHIMEDES
Run Processing Pipelines

Tip: Validate your dataset before uploading to identify missing files or naming issues.

Understanding the BIDS structure

Example BIDS dataset:
				
					MyStudy/

dataset_description.json
participants.tsv

sub-001/
    anat/
        sub-001_T1w.nii.gz

    func/
        sub-001_task-rest_bold.nii.gz

    dwi/
        sub-001_dwi.nii.gz
Folder Contains
anat Structural MRI
func Functional MRI
dwi Diffusion MRI
fmap Functional map
pet PET (Positron Emission Tomography)
eeg EEG (Electroencephalogram)
meg MEG (Magnetoencephalography)

Note: The above list includes the most common modality folders, but it is not a complete list of BIDS data modalities supported.

For a complete list of supported data types, folder structures, and naming conventions, refer to the official BIDS Specification.

Integrating BIDS with ARCHIMEDES

ARCHIMEDES supports BIDS-formatted datasets to facilitate:

Standardized data ingestion
Automated validation
Reproducible processing pipelines
Consistent data management
Secure data sharing
Before Uploading

ARCHIMEDES provides access to the BIDS Validator through its integrated CBRAIN environment, allowing users to verify that their datasets conform to the BIDS specification before processing or analysis.

Some Frequently Asked Questions

No. Several tools can automatically convert datasets into BIDS. Browse the available tools here.  

  • No. BIDS now supports many neuroimaging and physiological data types, including EEG, iEEG, MEG, behavioural data, PET, microscope data, motion-captured data, NIRS, and MRS. Different modality templates can be browsed here.  
  • There are also existing and in-progress BIDS Extension Proposals (BEPs), which are community driven processes to add a new modality or set of data types to the BIDS specification.  
  • Existing BIDS converter tools cover data from MRI, MRS, PET, MEG/EEG, fNIRS, and physiological data. 
  • There also exist tutorials for Arterial Spin Labelling data, iEEG data, MRI data, and PET data conversion 

Tools and Resources

BIDS Getting Started

A comprehensive introductory guide for beginners.

BIDS Validator

Verify your dataset’s compliance with standard formatting.

dcm2niix

Standard tool for converting DICOM formats to NIfTI.

BIDS Specification

The official, community-driven standard documentation.

HeuDiConv

Flexible DICOM converter for organizing brain imaging data into structured directory layouts

Additional tools

Explore tools for querying datasets, managing metadata, data annotation, analysis, and more.