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Experiments in neuroscience result in complex data that can be arranged in many different ways. For a long time, there was no consensus how to organize and share experimental data. Even two researchers working in the same lab could opt to arrange their data in a different way. Lack of consensus (or a standard) leads to misunderstandings and time wasted on rearranging data or rewriting scripts expecting certain structure. With the Brain Imaging Data Structure (BIDS), we describe a simple and easy to adopt way of organizing neural and associated, such as behavioral, data.
BIDS was heavily inspired by the format used internally by the OpenfMRI repository that is now known as OpenNeuro. While working on BIDS we consulted many neuroscientists to make sure it covers most common experiments, but at the same time is intuitive and easy to adopt. The specification is intentionally based on simple file formats and folder structures to reflect current lab practices and make it accessible to a wide range of scientists coming from different backgrounds.
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.
FAIR-ness of BIDS¶
A key motivation for the BIDS structure is creating an easy machine and human parsable structure for research data. By facilitating both the re-use of the data through standards of data structure while maintaining the clarity of what data is available to the user, BIDS provides an elegant solution to the findability, accessibility, interoperability, and reusability of research data and their derivatives.
Tools¶
BIDS Validator¶
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The BIDS Validator is a tool that checks if a dataset is compliant with the BIDS standard. The validator is available for use within several different environments to best suit individual user preferences and use cases, those versions are:
A web browser based version
Command line version
Docker based version
A python library installable from pypi or conda-forge
Instructions to install and use these versions can be found within the quickstart guide at the BIDS Validator repository.
Nipoppy¶
Nipoppy is a framework to facilitate the lifespan management of a project where you plan to utilize BIDS.
Please read more on the Nipoppy page.
References¶
Gorgolewski, K. J., Auer, T., Calhoun, V. D., Craddock, R. C., Das, S., Duff, E. P., ... & Poldrack, R. A. (2016). The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Scientific data, 3(1), 1-9.
Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., ... & Mons, B. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific data, 3(1), 1-9.