I am in the process of analyzing my multi-echo data through fmriprep and then through tedana. My fmriprep is on the run right now, and I would like to make sure I am good to go for the slice time correction before running tedana.
If my slice times look like below inside my json file (not interleaved), is there any correction to be made in the first place? Currently I have set my fmriprep to ignore slice time correction. Should I rerun my fmriprep with setting the slice time as 0? I was unsure if ignoring the slice time correction would just automatically take the file as is.
Slice timing and multi-echo considerations are not related to one another. If the BIDS validation report does not have any issues (for example, it will tell you if there is a slice time greater than your repetition time), you should be good to go.
I am not sure what you mean by this. Do you mean the —slice-time-ref 0? That is more a consideration for your general linear modeling, to make sure event timings are adjusted to what your slice timing interpolates to. I generally like to set mine as 0 or start in case softwares do not have the capability to adjust event times easily.
It seems like I am not getting this error, so I think I should be good. It seems like I was a little confused by the text in the tedana Q&A section. I appreciate your explanation! Thank you.
I was reading through the tedana Processing of multi-echo fMRI, where I assumed slice time correction should be applied for all 3 echos before running tedana.
