fmriprep

fmriprep is an fMRI preprocessing pipeline designed to provide an easily accessible interface regardless of scan acquisition parameters while requiring little user input. It performs minimal preprocessing, steps generally accepted to be necessary for any fMRI analysis pipeline. These include coregistration, normalization, unwarping, noise component extraction, segmentation, skullstripping etc. In order to run certain steps, it also performs automatic surface reconstruction through FreeSurfer. fmriprep is similar in scope to other minimal preprocessing pipelines like the HCP Pipelines.

To perform preprocessing, fmriprep uses tools from a variety of well-known software packages such as FSL, ANTs, AFNI, and the aforementioned FreeSurfer. Which tools are chosen for which steps were determined by the fmriprep creators. The tools used will be updated and changed as newer and better software is available.

For full information on fmriprep, please read their ReadTheDocs.