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., http://enigma.ini.usc.edu/protocols/imaging-protocols/).
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,
Jamie.
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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.
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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 (https://github.com/nimh-mbdu/fmriprep_qa_guide).
Cheers,
Nick
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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.
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During Googling, this thread comes up and I was wondering the same thing (five years after original post) so maybe it’s a good place to check in and see what the latest resources are w.r.t. doing QC on fmriprep. Best guide you’ve seen?
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I don’t have anything new to report… the things posted above are what we often use.
But maybe others will chime in with new bits!?
Not exactly an answer to the original question, but this protocol paper aimed at MRIQC outputs might be useful: https://www.biorxiv.org/content/10.1101/2024.10.21.619532v1