Multiecho pipeline

[TamerGezici]

Hi,

It seems like I will be needing to use a multiecho sequence for one of our studies. I believe aa does not support multiecho processing.

I see that people use fmriprep with TEDANA for ME. It seems the workflow goes like: some prep steps -> TEDANA -> more prep steps .... and so on.

I was thinking if it would be feasible to imitate this and use SPM for preprocessing. So we imitate fmriprep's prep steps, and start the necessary steps using SPM, add TEDANA as an aa module, and then continue the rest with SPM.

Alternatively, add fmriprep as an aa module, add TEDANA as a module, and do all preprocessing in fmriprep and then pick the outputs of fmriprep and continue on with analysis from there.

I can't decide which would be a feasible option (if any at all)

[tiborauer]

Both approaches could work depending on how much you prefer fmriprep over aa for preprocessing and what preprocessing you consider before and after TEDANA. I prefer aa for preprocessing for better flexibility and transparency and would like to see TEDANA as a module.
However, if you would rather use fmriprep, then I am unsure whether you want to use aa as a pipeline because nipype might be more efficient for a Python-dominated workflow with a few steps.