Hey Taylor,
First off, thanks for answering basically all of my TEDANA questions so far by the way.
I am using fmriprep version 21.0.1 for the initial preprocessing with the --me-output-echos flag. These echos were the input for my tedana workflow. It’s good to know there may be a " double-unwarping" in the optimally combined data so I should definitely take the extra step of unwarping and registering the data myself.
To do all of that, it seems like I could just use a similar command as shown in the this post linked in the fmriprep issue you linked. The only thing different is that instead of files looking like space-T1w_desc-preproc_bold.nii.gz mine would look like ‘space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz’. That would be lovely as it wouldn’t require any data from scratch and I could still use the same fmriprep container to apply the transform.
Great that was my basic intuition I just wasn’t sure if the de-noising used information from the individual echos other than Good point on orthogonalizing the components at very least with other confounds. I was thinking I would take an approach similar to what @dvsmith describes at the end of that aggressive vs. nonaggressive post with tedana noise components, anatomical CompCor (for spatially diffuse noise), cosines, and non steady states in my GLM. Though I understand I’ll be trading off temporal degrees of freedom.
Thanks again for the help