Hi Gershon,
I don’t believe that fMRIPrep labels the output preprocessed file as “optimally combined,” but it shouldn’t have echo-1 in the filename. Is that the case?
Currently, fMRIPrep doesn’t output the echo-specific images, which is why we recommend collecting the relevant files from fMRIPrep’s working directory and moving them into the output directory. We have some provisional code available here, although it’s currently just a notebook tailored to our project. We plan to convert it into a more general function soon, but you can almost certainly adapt it yourself to work with your own data structure. We have tested the code (and it looks good), but haven’t checked too deeply against fMRIPrep’s code, so we’re not 100% sure we’re grabbing the right files.
Regarding the field maps, it looks like you’re using --force-syn. That would force fMRIPrep to use field map-less distortion correction. I’m not sure about the sbref files. Are you sure it’s not using them? Can you share the captured stdout?
Best,
Taylor