Reproducible Tract Profiles pipeline.
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.
RTP uses parts of these tools (depending on the selected options):
- mrTrix 3
- mrVista, mrDiffusion and AFQ
- Ensemble Tractography (ET)
- LiFE/SIFT2(TODO)
- ANTs
- SPM
The documentation is in the wiki:
- Installation
- Pipeline documentation
- Parameter recommendations: differences in acquisition sequences or subject populations require to use different parameters, in this page we collect the parameters and pipeline versions we used for better results.
- Reporting and citation In this wiki page we include examples of how to report and cite RTP and all the included tools, it will change depending on the selected tools.
- TO-DO list