Abstract
The recent and growing focus on reproducibility in neuroimaging studies has led many major academic centers to use cloud-based imaging databases for storing, analyzing, and sharing complex imaging data. Flywheel is one such database platform that offers easily accessible, large-scale data management, along with a framework for reproducible analyses through containerized pipelines. The Brain Imaging Data Structure (BIDS) is the de facto standard for neuroimaging data, but curating neuroimaging data into BIDS can be a challenging and time-consuming task. In particular, standard solutions for BIDS curation are limited on Flywheel. To address these challenges, we developed “FlywheelTools,” a software toolbox for reproducible data curation and manipulation on Flywheel. FlywheelTools includes two elements: fw-heudiconv, for heuristic-driven curation of data into BIDS, and flaudit, which audits and inventories projects on Flywheel. Together, these tools accelerate reproducible neuroscience research on the widely used Flywheel platform.
Highlights
Many fields in science are grappling with failures of scientific reproducibility (Botvinik-Nezer et al, 2020)
The FlywheelTools toolkit allows users to follow a reproducible workflow for Brain Imaging Data Structure (BIDS) curation and auditing of their data
The first tool, fw-heudiconv2, is a multi-purpose commandline interface and Flywheel gear designed for BIDS curation on Flywheel (Figure 1)
Summary
Many fields in science are grappling with failures of scientific reproducibility (Botvinik-Nezer et al, 2020). Given the high dimensionality of the data, the need for complex image processing, and a plethora of analytic techniques, this crisis is acute for neuroimaging research. Major academic centers and large consortia have increasingly adopted platforms that leverage database technologies that have become standard in other fields. In addition to providing functionality for searching and categorizing complex source data, imaging databases enhance reproducible research by providing a clear audit trail of image processing applied to the data and its results, including both derived images and other data. The FlywheelTools commercial platform Flywheel has become widely used due to its modern technology, ease of use, and scalability
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