fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
This sounds like the trickiest one to implement cleanly, as it basically means somehow exposing fine-tuning of mri_vol2surf at the command line or in a configuration file. mri_vol2surf --reg-header will get you the GIFTI files, but re-centering them requires a variation on normalize_surfs.
From #658