Date: November 5 2020
Summary: An overview of the BIDS style for Brain Imaging Data.
Keywords: ##zettel #bids #neuroscience #brain #imaging #archive
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A core problem regarding reproducible neuroscience is that there has been no widely adopted standard for describing data from an imaging experiment. This renders sharing and reusing data difficult.[1] Furthermore, it complicates automation and quality assurance.
The BIDS format was inspired by the work done by the OpenNeuro community to easily share and structure their data regarding pertaining to neuroscientific research. It enables development of automated tools to operate on datasets. [1] Common standards minimize curation! Helps those not involved to effectively understand the data.
Raw data derivatives should be separate from source data.
The NIfTI image file format was selected as it is the most ubiquitous across neuroimaging software.BIDS requires users to provide additional meta information in a sidecar JSON file.
Metadata is generally stored as an array in tab-delimited values.
JSON files are used for storing key/value pairs.
The key names follow a fixed dictionary in the specification.
Neuroimaging: brain imaging to gain quantitative brain data. [1]
Error reduction: errors attributed to misunderstanding data.
Provenance: information regarding actions or those involved in producing an object. It can be used to form assessments about its valour.
Zelko, Jacob. Brain Imaging Data Structure (BIDS). https://jacobzelko.com/11052020174635-brain-imaging-structure. November 5 2020.
[1] K. J. Gorgolewski et al., “The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments,” Sci Data, vol. 3, no. 1, p. 160044, Dec. 2016, doi: 10.1038/sdata.2016.44.