Hi Kevin,

The coregistration T1-EPI is done on the average of all functional sessions/runs, after correction for motion correction. So the same transformation applies to all run. If one run is better coregistered than others, that means that it is actually the motion correction that did not work properly. You can have a look at the folder quality_control//motion_correction . The file tab_coregister_motion.csv contains some info about the between-runs motion correction. The only time I've seen that step fail, the investigator had actually mixed up the datasets from two different subjects. If you actually found that that the datasets are correct and this step failed, please send me an email with the location of the database so I can have an in-depth look at it, I'd be really interested in understanding what went wrong. 

Regards,

Pierre