Basic checks
Check for CommonArtefacts
Run DataDiagnostics - this is done by most AutomaticAnalysisIntroduction recipes if you choose to use this path
If you are unfortunate enough to find bad data, consider whether to RemoveBadScans
Typical pre-processing stages
These are the stages typical to most analyses
Slice timing - correcting for the fact that different slices in the brain are acquired at different times
Undistort EPIs using field maps - usually no longer necessary on data from the Siemens scanner
Motion correction - correcting for subject movement through an fMRI scan, sometimes called realignment