fMRIprep QC protocol?

Hello all,

I was wondering if anyone had developed a standardized protocol for dealing with the outputs of fMRIprep (the actual NIfTI files, or the HTML)? I was trying to train staff and students in my lab on fMRIprep checks, and was starting to develop some documents; I, however, thought I would see if others had compiled something similar and/or there were consensus documents for dealing with outputs?

The best analogs would be something like the guides that ENIGMA develop for Freesurfer troubleshooting / QC (e.g.,

I searched on the forum a bit and didn’t find any relevant posts; I also looked on readthedocs, but again no luck. Any thoughts are deeply appreciated!

Thanks much,


I have not gone for a deep dive on the interweb for that but I am sure that there are a few things being done around that. And there is a market for this for sure.

One I am aware of and that is mostly geared towards motion is this one:

Hope it helps.


As a new addition to the neuroscience community, and someone that is preparing for my first run through of #fmriprep, I have the same question.

EDIT: I dove into this search a little more and was able to find a similar thread (fMRIPrep Tutorial), which led me to @Shotgunosine’s guide (




Not a protocol per se, but I’ve been working on a draft of some QC documentation for fMRIPrep. Currently lives here.

I unfortunately haven’t been able to devote time to finish it yet, and would absolutely welcome any contributions based on your experiences training staff and students to look at the reports.