In recent BIDS releases, we have a separate suffix for those volumes. The idea is, as part of curation, you should split them out of the _bold NIfTIs and use the _noRF suffix. I’ve never tried removing DICOMs- I just convert to NIfTI and split after.
If you plan to run NORDIC on these data, then you have to reconcatenate them, explicitly set the slope and intercept to 1 and 0, respectively, process them with NORDIC, and then resplit them. It’s a complicated workaround, so it might be easier for you to run NORDIC on the full NIfTIs first, then split the noRF volumes out after the files have been denoised.
Neither fMRIPrep nor tedana can leverage phase data yet, but I’m hopeful that’ll change. Just make sure you have the part-mag in your magnitude filenames and part-phase in your phase filenames.
There are a bunch of cool applications for phase data though, including: better thermal noise removal with NORDIC or MP-PCA (thermal noise is Rician in magnitude-only data but Gaussian in complex-valued data, which is apparently better); extraction of phase-based confounds like HighCor (Curtis and Menon, 2014) and respiratory signal (Jaffray et al., 2024); calculation of phase-based derivatives like phase jolt (see Applying LN2_PHASE_JOLT to multi-echo data); phase regression (e.g., Stanley et al., 2021); complex ICA (Calhoun et al., 2002), and complex-valued modeling (e.g., Adrian, Maitra, & Rowe, 2018).
There are also some pretty cool multi-echo-specific applications, like better R2* estimation (Cohen-Adad et al., 2012); dynamic distortion correction with the MEDIC method (Van et al., preprint); functional quantitative susceptibility mapping (Balla et al., 2014); and EPI-QSM (basically just the fQSM time series averaged over time) (Kiersnowski et al., 2024).
Sadly, most of those applications aren’t supported in popular pipelines like fMRIPrep. I’m hoping to at least implement some of the post-processing methods (phase regression, phase jolt derivatives, etc.) into a BIDS App at some point (see GitHub - nipreps/fmripost-phase: An attempt at an fMRIPost workflow for handling phase data · GitHub), but haven’t had much time to dedicate to it yet.