Benefits

By using this standard you will benefit in the following ways:

Converters

MRI and PET converters

Name Expected input Language Distribution Comment Updated
bidsify
  • DICOM
  • PAR/REC
  • Python
Tool to convert source MRI datasets to BIDS-compatible datasets.
GitHub last commit
bidskit
  • DICOM
  • Python
Utility functions for working with DICOM and BIDS neuroimaging data.
GitHub last commit
BMAT
  • DICOM
  • Python
GitHub last commit
Data2Bids
  • not DICOM
  • Python
Converts MRI files from extension supported by nibabel into NIfTI and convert them to BIDS
GitHub last commit
Dcm2Bids
  • DICOM
  • Python
converts DICOM files using dcm2niix into BIDS
GitHub last commit
HeuDiConv
  • DICOM
  • Python
A flexible DICOM converter for organizing brain imaging data into structured directory layouts
GitHub last commit
OpenfMRI2BIDS
Convert OpenfMRI dataset to BIDS
GitHub last commit
ReproIn
  • Python
HeuDiConv-based turnkey solution: a setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners.
GitHub last commit
XNAT2BIDS
  • shell
Simple xnat pipeline to convert DICOM scans to BIDS-compatible output (nii+json).
GitHub last commit
Horos (Osirix) export plugin
  • objective C
Horos plugin for BIDS output.
GitHub last commit
BIDScoin
  • DICOM
  • PAR/REC
  • physiological
  • PET
  • Python
BIDScoin converts your source-level neuroimaging data to BIDS
GitHub last commit
BIDSme
  • DICOM
  • Nifti
  • Brain Vision
  • Python
GitHub last commit
BrkRaw
  • Bruker MRI scanner data
  • Python
For a preclinical Bruker MRI scanner
GitHub last commit
Clinica
  • ADNI
  • AIBL
  • NIFD
  • OASIS
  • OASIS-3
  • Python
GitHub last commit
dac2bids
  • DICOM
  • Python
Create a BIDS structure for a DICOM folder.
GitHub last commit
Autobids
  • DICOM
Automated Dicom to BIDS and pipelines using compute canada. From the Centre for Functional and Metabolic Mapping (CFMM) at Western’s Robarts Research Institute.
GitHub last commit
PET2BIDS
  • DICOM
  • ECAT
  • MATLAB
  • Python
Helps you convert your PET data! raw PET scanner files (for example ecat, dicom) and additional side file like excel sheets.
GitHub last commit
Explore ASL
  • DICOM
  • Nifti
  • MATLAB
Convert DICOM and NIFTI data to the ASL-BIDS format.
GitHub last commit
SAMRI
  • Bruker ParaVision
  • NIfTI
  • Python
  • shell
Full stack Small Animal MRI data analysis package, including the `bru2bids` repositing pipeline, which can convert Bruker archives to the BIDS format. From the ETH and University of Zurich, with collaboration from MIT and Dartmouth College.
GitHub last commit
BIDSconvertR
  • DICOM
  • R
The BIDSconvertR R package provides a user-friendly workflow with graphical user interfaces. It conists of the following steps: (i) convert DICOM data to NIfTI data using dcm2niix (ii) structure this data according to the BIDS specification (iii) provide the papayaWidget viewer for inspecting the images
GitHub last commit

EEG, MEG, iEEG converters

Name Expected input Language Distribution Comment Updated
BIDSme
  • DICOM
  • Nifti
  • Brain Vision
  • Python
GitHub last commit
MNE-BIDS
  • raw MEG for BIDS conversion
  • raw EEG for BIDS conversion
  • raw iEEG for BIDS conversion
  • raw NIRS for BIDS conversion
  • BIDS dataset for reading
  • Python
MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.
GitHub last commit
EEGLAB
  • EDF
  • BDF
  • Brain Vision Exchange Format
  • EEGLAB .set files
  • MATLAB
See plugins
GitHub last commit
FieldTrip - data2bids
  • any EEG or MEG file format
  • NBS Presentation logfiles
  • DICOM
  • nifti
  • MATLAB
GitHub last commit
Biscuit
  • Python
GUI for easy MEG to BIDS conversion
GitHub last commit
sovabids
  • Python
A Python package for the automatic conversion of EEG datasets to the BIDS standard, with a focus on making the most out of metadata.
GitHub last commit
EEG2BIDS
  • Javascript
  • Python
A tool for converting raw EEG and iEEG data into the BIDS standard data structure, prepared for LORIS (Longitudinal Online Research and Imaging System).
GitHub last commit

'From BIDS' converters

Converters that take a BIDS dataset as input to convert it into something else. Not mentioned here are the many softwares that can import a BIDS data as data structure they are more familiar with.

Name Expected input Language Distribution Comment Updated
BIDS2ISATab
  • BIDS
  • Python
Extract ISA-Tab compatible metadata from BIDS
GitHub last commit
BIDSto3col
  • BIDS
  • shell
  • Python
Reads BidsTSV and then creates 3 column event files, one per event type if a "trial_type" column is found.
GitHub last commit
BIDS2NDA
  • BIDS
  • Python
Extract NIHM Data Archive compatible metadata from BIDS
GitHub last commit
bids2xar - for XNAT import
  • BIDS
  • Python
Convert BIDS data set into XNAT XAR bundles
GitHub last commit
BIDS2NIDM
  • BIDS
  • Python
This program will convert a NIDM-Experiment RDF document to a BIDS dataset.
GitHub last commit
AFNI BIDS-tools
  • BIDS
  • shell
  • Python
ARCHIVED - Scripts, tools, and documents on creating, parsing, and working with BIDS-structured data sets.
GitHub last commit

Physiological data converters

Name Expected input Language Distribution Comment Updated
BIDScoin
  • DICOM
  • PAR/REC
  • physiological
  • PET
  • Python
BIDScoin converts your source-level neuroimaging data to BIDS
GitHub last commit
phys2bids
  • Acqknowledge
  • Labchart
  • Python
Python3 library to format physiological files in BIDS.
GitHub last commit

Miscellaneous

Not exactly BIDS converters but are common tools that can used by other BIDS converters.

Name Expected input Language Distribution Comment Updated
convert-eprime
  • E-Prime log files
  • Python
Python functions to convert E-Prime files to csvs. Not currently being developed.
GitHub last commit
DCM2NIIx
  • C++ (compiled versions available from NITRC)
dcm2nii DICOM to NIfTI converter
GitHub last commit
DICM2NII
  • DICOM
  • MATLAB
dcm2nii DICOM to NIfTI converter
GitHub last commit
sim2bids
  • network and coordinate files expected_input:
    • CSV/TSV/DAT/Numpy
    • arrays/HDF5,
    • zip folders,
    • and code files in MATLAB/Python/R
  • Python
GUI to easily convert simulation results to BIDS format, according to BEP 34 .
GitHub last commit

Software currently supporting BIDS:

A description of how to build containerized apps supporting BIDS inputs can be found in the paper published in PLOS Computational Biology.

Other Tools