5. Snakebids: Flexible Input Interfaces for BIDS Apps

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The increasing popularity of the Brain Imaging Data Structure (BIDS) specification for neuroimaging data (Gorgolewski et al., 2016) has led to a flourishing of workflows known as BIDS Apps (Gorgolewski et al., 2017). With a standardized data structure enforced by BIDS, a wide variety of workflows can be easily applied to neuroimaging datasets from any arbitrary source. This not only simplifies app development, but makes it easier to share generic analysis code for future replication. Nevertheless, even with the BIDS specification, a wide diversity of data formatting persists, especially for derived files. This makes it challenging to design BIDS Apps consuming derivative files with nonstandard naming conventions. To ensure workflows remain generic even in the absence of specific naming conventions, we present snakebids, a Python library leveraging pybids to create generic interfaces between BIDS Apps and datasets.