Is there any documentation for how to do manual preprocessing of the data? I used the pipeline, and that worked for the majority of my participants, however after various QA measures it's clear that something went wrong for several of my participants (I'm working with older brains so this might be part of the issue). For example, when assessing the single slice for all subjects montage for the functional data the brains are not showing the same slice across subjects (in fact some look coronal while others look transverse), as well as issues with gray and white matter segmentation. 

Thanks so much!