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 |
|---|---|---|---|
| ancp-bids | Python |
A Python package to read/write/query/validate BIDS datasets. |  |
| bids2table | Python |
bids2table is a library for efficiently indexing and querying large-scale BIDS neuroimaging datasets and derivatives. |  |
| bids-matlab | MATLAB Octave |
MATLAB/Octave tools to interact with datasets conforming to the BIDS format |  |
| bidser | R |
Working with Brain Imaging Data Structure in R |  |
| BIDSHandler | Python |
Library for loading and manipulating BIDS compatible MEG data |  |
| PyBIDS | Python |
Python package to quickly parse / search the components of a BIDS dataset. It also contains functionality for running analyses on your data. |  |
| 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 |
|---|---|---|---|
| bids2cite | Python |
package to interactively update dataset_description.json and generate citation files (for example datacite.yml) for BIDS datasets. |
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| 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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| 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) online tools | wesbite |
Online tools for annotation, validation, summary, and assembly of event file contents and annotations. |  |
| Hierarchical Event Descriptors (HED) Python tools | Python |
HED libraries supporting schema development as well as annotation, validation, and analysis. |  |
| 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 |  |
| Lead-DBS | MATLAB |
A toolbox facilitating Deep Brain Stimulation electrode reconstructions and computer simulations supports BIDS conversion and ingestion of BIDS datasets. |  |
| 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. |  |
| PRFmodel | a set of tools to fit population receptive field models to BIDS datasets |  |
Others
| Name | Language | Description | Updated |
|---|---|---|---|
| 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-cfood | Python |
a module to handle BIDS dataset for the caosDB data crawler |  |
| 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. |  |
| bids stats model | Python |
Validate BIDS statistical model. To learn more the BIDS stats model website |  |
| 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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