Reproducible Tract Profiles (RTP): from diffusion MRI acquisition to publication

Abstract

Reproducible Tract Profiles (RTP) comprises a set of methods to manage and analyze diffusion weighted imaging (DWI) data for reproducible tractography. The tools take MRI data from the scanner and process them through a series of analysis implemented as Docker containers that are integrated into a modern neuroinformatics platform (Flywheel). The platform guarantees that the entire pipeline can be re-executed, using the same data and computational parameters. In this paper, we describe (1) a cloud based neuroinformatics platform, (2) a tool to programmatically access and control the platform from a client, and (3) the DWI analysis tools that are used to identify the positions of 22 tracts and their diffusion profiles. The combination of these three components defines a system that transforms raw data into reproducible tract profiles for publication.\n\nGraphical abstractReproducible Tract Profiles (RTP) comprises a set of methods to manage and analyze diffusion weighted imaging (DWI) data for reproducible tractography. The RTP methods comprise two main parts. O_LIServer side software tools for storing data and metadata and managing containerized computations.\nC_LIO_LIClient side software tools that enable the researcher to read data and metadata and manage server-side computations.\nC_LI\n\nThe server-side computational tools are embedded in containers that are linked to a JSON file with a complete specification of the computational parameters. The data and computational infrastructure on the server is fully reproducible.