I have encountered a similar issue and thought this might be a good place to seek help.
I have the information about the different TEs, which I included in the phasediff.json file, according to the specs,
and the output from Siemens (converted to .nii, 1 screenshot below, due to the limit of one picture), yet when trying to run fmriprep I got the following error-
“traits.trait_errors.TraitError: The trait ‘in_files’ of an IntraModalMergeInputSpec instance is an existing file name, but the path ‘/snapshot/data/sub-001/fmap/sub-001_magnitude2.nii.gz’ does not exist.”
Thanks in advance for your help!