This is the OGRE (One-Step General Registration and Extraction) pipeline, which is intended to be general-purpose for fMRI data (especially task fMRI) preprocessing. OGRE integrates FSL and FreeSurfer tools for registration, brain extraction, and preprocessing, for subsequent FSL FEAT statistical analysis on Mac or Linux.
Installation/prerequisites and general documentation are available in the "documentation" directory.
By Mark McAvoy & Benjamin Philip at Washington University, 2021-2025.
Preprint: https://www.biorxiv.org/content/10.1101/2023.09.19.558290