Removing burn in before running tedana

[Cameron.T.Ellis]

Hello,

Should the burn in (AKA dummy cycles, AKA disdaq) be removed before running tedana? I have run it both ways on a few participants and there was no systematic difference, so wanted to hear if there is a principled reason one way or the other.

Thanks in advance,
Cameron

[dowdlelt]

This has come up before - we recommend discarding them and I’d likely stick with that even if the effect seems to be minimal.

How does tedana deal with non steady state / dummy scans? (fMRIPrep + tedana)

Welcome @sjshim and thank you for asking this question. These volumes definitely should not go into tedana. I think adding a --skipvols option might be a bit tricky since we can’t remove volumes for the ICA and then add them back in for the denoising step. That means we’d either be keeping them at the beginning of the volume untouched or using tedana to remove those volumes. My inclination is that they should be removed as part of the preprocessing pipeline, not tedana because, for the sake of…

[Cameron.T.Ellis]

Brilliant, thank you!