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 reproducibility, you’d want your preprocessing pipeline and not some cog in the pipeline to keep track of when a volume is removed and how that affects other steps in the pipeline.
T1 has been estimated from the non-steady state volumes. See: Bodurka, J., Ye, F., Petridou, N., Murphy, K. & Bandettini, P. A. Mapping the MRI voxel volume in which thermal noise matches physiological noise–implications for fMRI. Neuroimage 34, 542–9 (2007)
It might be possible to use the non-steady state volumes and multi-echo information to get a T2* estimate, and I vaguely remember reading something, but can’t remember the reference right now.
Dan