Benefits
By using this standard you will benefit in the following ways:
- It will be easy for another researcher to work on your data. To understand the organization of the files and their format you will only need to refer them to this document. This is especially important if you are running your own lab and anticipate more than one person working on the same data over time. By using BIDS you will save time trying to understand and reuse data acquired by a graduate student or postdoc that has already left the lab.
- There is a growing number of data analysis software packages that can understand data organized according to BIDS.
- Databases such as OpenNeuro.org, LORIS, COINS, XNAT, SciTran, and others will accept and export datasets organized according to BIDS. If you ever plan to share your data publicly (nowadays some journals require this) you can speed up the curation process by using BIDS.
- There are validation tools (also available online) that can check your dataset integrity and let you easily spot missing values.
Software currently supporting BIDS:
- BIDS Apps (a growing set of portable containerized data processing pipelines that understand BIDS datasets)
A description of how to build containerized apps supporting BIDS inputs can be found in the paper published in PLOS Computational Biology.
Converters
MRI and PET converters
Name | Data type | Expected input | Language | Distribution | GUI | Documentation | Comment | License | Updated |
---|---|---|---|---|---|---|---|---|---|
bidsify | MRI | DICOM, PAR/REC | Python | Tool to convert source MRI datasets to BIDS-compatible datasets. | 2019 | ||||
bidskit | MRI | DICOM | Python | doc | Utility functions for working with DICOM and BIDS neuroimaging data. | MIT | 2019 | ||
Data2Bids | MRI | not DICOM | Python | Converts MRI files from extension supported by nibabel into NIfTI and convert them to BIDS | MIT | 2019 | |||
Dcm2Bids | MRI | DICOM | Python | doc | converts DICOM files using dcm2niix into BIDS | GPL-3.0 | 2021 | ||
HeuDiConv | MRI | DICOM | Python | doc | A flexible DICOM converter for organizing brain imaging data into structured directory layouts | Apache 2.0 | 2021 | ||
OpenfMRI2BIDS | MRI |
|
Convert OpenfMRI dataset to BIDS | 2018 | |||||
ReproIn | MRI | Python | HeuDiConv-based turnkey solution: a setup for automatic generation of shareable, version-controlled BIDS datasets from MR scanners. | MIT | 2021 | ||||
XNAT2BIDS | MRI | shell |
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Simple xnat pipeline to convert DICOM scans to BIDS-compatible output (nii+json). | 2018 | ||||
Horos (Osirix) export plugin | objective C |
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true | Horos plugin for BIDS output. | GPL-3.0 | 2018 | |||
BIDScoin | MRI, phsyiological, behavioral, PET | DICOM, PAR/REC, physiological, PET | Python | true | doc | BIDScoin converts your source-level neuroimaging data to BIDS | GPL-3.0 | 2021 | |
BIDSme | MRI, EEG | DICOM, Nifti, Brain Vision | Python |
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doc | GPL-2.0 | 2021 | ||
BrkRaw | MRI | Bruker MRI scanner data | Python |
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true | For a preclinical Bruker MRI scanner | GPL-3.0 | 2021 | |
Clinica | data from ADNI, AIBL, NIFD, OASIS, OASIS-3 | Python |
|
doc | MIT | 2021 | |||
dac2bids | MRI | DICOM | Python |
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Create a BIDS structure for a DICOM folder. | 2017 | |||
Autobids | MRI | DICOM |
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Automated Dicom to BIDS and pipelines using compute canada. From the Centre for Functional and Metabolic Mapping (CFMM) at Western’s Robarts Research Institute. | 2021 | ||||
BIDS-converter | PET | DICOM, ECAT | MATLAB, Python |
|
false | Helps you convert your PET data! raw PET scanner files (for example ecat, dicom) and additional side file like excel sheets. | MIT | 2021 | |
Explore ASL | ASL | DICOM, Nifti | MATLAB |
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doc | Convert DICOM and NIFTI data to the ASL-BIDS format. | 2021 | ||
SAMRI | small-animal MRI | Bruker ParaVision, NIfTI | Python, shell |
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false | doc | 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. | 2021 | |
BIDSconvertR | MRI | DICOM | R |
|
true | doc | 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 | GPL-3.0 | 2022 |
EEG, MEG, iEEG converters
Name | Data type | Expected input | Language | Distribution | GUI | Documentation | Comment | License | Updated |
---|---|---|---|---|---|---|---|---|---|
BIDSme | MRI, EEG | DICOM, Nifti, Brain Vision | Python |
|
doc | GPL-2.0 | 2021 | ||
MNE-BIDS | MEG, EEG, iEEG | Either raw MEG, EEG, or iEEG data for conversion, or a BIDS dataset for reading | Python | false | doc | MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python. | BSD-3-Clause | 2022 | |
EEGLAB | MEG, EEG | EDF, BDF, Brain Vision Exchange Format, EEGLAB .set files | MATLAB |
|
See plugins | 2021 | |||
FieldTrip - data2bids | EEG, MEG, iEEG, behavioral, MRI (anat and func) | any EEG or MEG file format, NBS Presentation logfiles, DICOM, nifti | MATLAB |
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doc | GPL-3.0 | 2021 | ||
Biscuit | MEG | Python |
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true | doc | GUI for easy MEG to BIDS conversion | MIT | 2019 | |
sovabids | EEG | Python |
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doc | A Python package for the automatic conversion of EEG datasets to the BIDS standard, with a focus on making the most out of metadata. | 2021 | |||
EEG2BIDS | EEG | Javascript, Python |
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A tool for converting raw EEG and iEEG data into the BIDS standard data structure, prepared for LORIS (Longitudinal Online Research and Imaging System). | 2021 |
'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 | Data type | Expected input | Language | Distribution | GUI | Documentation | Comment | License | Updated |
---|---|---|---|---|---|---|---|---|---|
BIDS2ISATab | BIDS | Python |
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Extract ISA-Tab compatible metadata from BIDS | 2016 | ||||
BIDSto3col | TSV | BIDS | shell, Python |
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Reads BidsTSV and then creates 3 column event files, one per event type if a "trial_type" column is found. | 2016 | |||
BIDS2NDA | BIDS | Python |
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Extract NIHM Data Archive compatible metadata from BIDS | Apache-2.0 | 2020 | |||
bids2xar - for XNAT import | MRI | BIDS | Python |
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Convert BIDS data set into XNAT XAR bundles | 2017 | |||
BIDS2NIDM | BIDS | Python |
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This program will convert a NIDM-Experiment RDF document to a BIDS dataset. | 2021 | ||||
AFNI BIDS-tools | MRI | BIDS | shell, Python |
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ARCHIVED - Scripts, tools, and documents on creating, parsing, and working with BIDS-structured data sets. | 2019 |
Physiological data converters
Name | Data type | Expected input | Language | Distribution | GUI | Documentation | Comment | License | Updated |
---|---|---|---|---|---|---|---|---|---|
BIDScoin | MRI, phsyiological, behavioral, PET | DICOM, PAR/REC, physiological, PET | Python | true | doc | BIDScoin converts your source-level neuroimaging data to BIDS | GPL-3 | 2021 | |
phys2bids | phsyiological | Acqknowledge, Labchart | Python | doc | Python3 library to format physiological files in BIDS. | Apache-2.0 | 2021 |
Miscellaneous
Not exactly BIDS converters but are common tools that can used by other BIDS converters.
Name | Data type | Expected input | Language | Distribution | GUI | Documentation | Comment | License | Updated |
---|---|---|---|---|---|---|---|---|---|
convert-eprime | behavioral | E-Prime log files | Python |
|
Python functions to convert E-Prime files to csvs. Not currently being developed. | MIT | 2020 | ||
DCM2NIIx | DICOM, PAR/REC | C++ (compiled versions available from NITRC) |
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dcm2nii DICOM to NIfTI converter | 2021 | ||||
DICM2NII | DICOM | DICOM | MATLAB |
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dcm2nii DICOM to NIfTI converter | BSD-2 | 2021 |
Quality Assessment
Other Tools
- Automatic Analysis (multimodal MATLAB toolbox processing fMRI, DTI/DKI, and M/EEG)
- BIDSHandler (Python module allowing complete manipulation of BIDS data)
- Brainstorm (MEG/EEG analysis package)
- C-PAC (Configurable Pipeline for the Analysing Connectomes)
- FMRIPREP (preprocessing workflow)
- OpenNeuro (repository)
- PyBIDS (Python module to harmonize access and manipulation)
- bids-matlab (MATLAB/Octave tools to interact with datasets conforming to the BIDS format)
- GUI dataset description generator (GUI form that generates dataset_description.json)