CBIG fMRI preprocessing pipeline: compatibility with BIDS format

[Remi-Gau]

Submitted by CBIG group*

BIDS (Brain Imaging Data Structure) format provides a standard way for neuroimaging investigators to share their data and gains an increasing number of users. Our group is maintaining an fMRI preprocessing pipeline that allows flexible preprocessing order. However, currently this pipeline is not very compatible with BIDS format. During OHBM hackathon, we would like to modify CBIG preprocessing pipeline so that it can automatically handle input data in BIDS format, and also reorganize input data into BIDS format if they are not.

The steps to achieve this goal:

• Understand the folder structure of BIDS format;
• Identify what are the files needed for CBIG preprocessing pipeline and how to locate them in BIDS format;
• Write scripts to grab the needed files and pass to current preprocessing scripts;
• Test on some data in BIDS format;
• Re-run some GSP (Brain Genomics Superstruct Project) subjects to make sure original functionality is not affected.

This upgrade will benefit people who are using (or plan to use) CBIG fMRI preprocessing code.