Tools
Indexing and querying
These tools help index the content of BIDS datasets and return a listing of files that match a certain query
(for example "Give me all the files from subject 01 and 13 for datatypes anat and eeg.")
| Name | Language | Description | Updated |
|---|---|---|---|
| BIDSHandler | Python |
Library for loading and manipulating BIDS compatible MEG data |  |
| EEGDash | Python |
Data-sharing resource for MEEG (EEG, MEG, iEEG) data enabling large-scale computational advancements. Aggregates datasets from 25 laboratories with over 27,000 participants including healthy subjects and clinical populations. Provides dataset catalog, search capabilities, and comprehensive API for programmatic access. Returns PyTorch Datasets for machine learning applications with support for BIDS-formatted datasets. |  |
| PyBIDS | Python |
Python package to quickly parse / search the components of a BIDS dataset. It also contains functionality for running analyses on your data. |  |
| LazyBIDS | Python |
Python package to interact with BIDS datasets in a pythonic way. A BIDS dataset is read to hierarchical pydantic models (e.g. dataset->subjects->sessions->scans), variables are accesibles as model properties, tables, SimpleITK Images and numpy arrays. Also serves as python client for lazybids-ui server. |  |
| ancp-bids | Python |
A Python package to read/write/query/validate BIDS datasets. |  |
| bids-matlab | MATLAB Octave |
MATLAB/Octave tools to interact with datasets conforming to the BIDS format |  |
| bids2table | Python |
bids2table is a library for efficiently indexing and querying large-scale BIDS neuroimaging datasets and derivatives. |  |
| bidser | R |
Working with Brain Imaging Data Structure in R |  |
| libBIDS.sh | bash |
A bash library used to parse BIDS datasets into a data structure suitable for use in shell pipelines. |  |
| rbids | R |
aims to make BIDS datasets more easily accessible for packages written in R |  |
File handling
These tools help you work with certain specific BIDS files or may help you rename them.
| Name | Language | Description | Updated |
|---|---|---|---|
| EEGBIDS standalone | MATLAB executable |
Standalone compiled MATLAB version of the EEG-BIDS plugin with a graphic interface wizard. Available as part of the compiled EEGLAB distribution (EEGBIDS executable on Mac, EEGBIDS.bat on Windows). Does not require a paid MATLAB license. Allows importing and exporting BIDS-formatted EEG/MEG/iEEG data and converting BIDS to NWB format for iEEG data. |  |
| File mapper | Python |
An easy tool to copy/move/symlink files from one directory to the other! Can be used to "convert" dataset to be BIDS compliant. |  |
| GUI dataset description generator | Python |
GUI form that generates dataset_description.json |
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| bids2cite | Python |
package to interactively update dataset_description.json and generate citation files (for example datacite.yml) for BIDS datasets. |
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| spm_2_bids | MATLAB Octave |
a tool convert SPM preprocessed output to BIDS derivatives (trying to follow BEP12) |  |
Data annotation
These tools make it easier to curate the metadata of your BIDS dataset.
| Name | Language | Description | Updated |
|---|---|---|---|
| Hierarchical Event Descriptors (HED) Python tools | Python |
HED libraries supporting schema development as well as annotation, validation, and analysis. |  |
| Hierarchical Event Descriptors (HED) online tools | website |
Online tools for annotation, validation, summary, and assembly of event file contents and annotations. |  |
| Hierarchical Event Descriptors (HED) browser-based tools | Javascript |
Browser-based validation of HED in BIDS datasets (no data upload). |  |
| LazyBIDS-ui | Python HTML |
FastAPI web server providing a GUI to explore (imaging) BIDS datasets interactively, also provides (XNAT-like) REST-API to access (parts of) datasets on a client machine. Uses NiiVue to view and navigate (3D) images in the browser. |  |
| neurobagel annotate | website |
This tool allows you to create a machine readable data dictionary in .json format for a tabular phenotypic file in .tsv format ("Data table"). |  |
Analysis
These packages or toolboxes are BIDS "friendly" and contain functionalities that will make your life easeir if you work with BIDS datasets.
| Name | Language | Description | Updated |
|---|---|---|---|
| Brainstorm | MATLAB |
MEG/EEG analysis package |  |
| EEGLAB EEG-BIDS plugin | MATLAB |
EEGLAB plugin for importing and exporting BIDS-formatted experiments. Handles conversion from multiple data formats including EEGLAB .set files, EDF, BDF, and Brain Vision Exchange Format. Supports EEG, iEEG, and MEG data with export to NWB format for iEEG data. | |
| EEGPrep | Python |
Python library to import and process BIDS datasets and output valid derivative BIDS. Implements the EEGLAB default pipeline in Python with Clean_rawdata and ICLabel for artifact removal, channel cleaning, and automated component classification. Made by the developers of EEGLAB. |  |
| Lead-DBS | MATLAB |
A toolbox facilitating Deep Brain Stimulation electrode reconstructions and computer simulations supports BIDS conversion and ingestion of BIDS datasets. |  |
| PRFmodel | a set of tools to fit population receptive field models to BIDS datasets |  |
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| mne-bids | Python |
collection of tools for converting magnetoencephalography (MEG) data into BIDS format, as well as some helper functions for creating the folders and metadata needed for a BIDS dataset. |  |
| mne-bids-pipeline | Python |
MNE-BIDS-Pipeline is a full-flegded processing pipeline for your MEG and EEG data. Under the hood, it uses MNE-Python. |  |
Others
| Name | Language | Description | Updated |
|---|---|---|---|
| BIDS-pydantic | Python |
Pulls a specified version of the BIDS schema and creates corresponding Pydantic models, which will provide BIDS data validation using Python type annotations. See also BIDS-pydantic-models. |  |
| babs | Python |
BIDS App Bootstrap (BABS) is a reproducible, generalizable, and scalable Python package for BIDS App analysis of large datasets. It uses DataLad and adopts FAIRly big framework. |  |
| bids stats model | Python |
Validate BIDS statistical model. To learn more the BIDS stats model website |  |
| bids-cfood | Python |
a module to handle BIDS dataset for the caosDB data crawler |  |
| clpipe | Python |
streamlined processing pipeline for MRI data centered around BIDS |  |
| cuBIDS | Python |
a Python package designed to facilitate reproducible curation of neuroimaging BIDS datasets |  |
| neurobagel query | website |
Neurobagel's query tool is a web interface for searching across a BIDS datasets based on various subject clinical-demographic and imaging parameters. |  |
| nipopy | Python |
Lightweight neuroimaging workflow manager to help with DICOM to BIDS conversion and running BIDS apps. |  |
| psychopy-bids | Python |
A psychopy plugin to help easily output a BIDS dataset, including events.tsv and beh.tsv files when running experiments with psychopy. |
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