Hi all, thanks for sharing the info so far. Not sure if other people have had success using the SyN/fieldmapless method recently but wanted to share some output from fmriprep 22.1.1 related to this topic to see if anyone else had similar experiences or recommendations. I have gradient echo func data with fieldmaps for each run (rev PE pair of spin echo vols linked to respective runs using b0FieldIdentifier/b0FieldSource in the jsons). Some fieldmaps have motion etc. so I wanted to compare the SyN approach to the PEPolar SDC.
–When running fmriprep with --ignore fieldmaps and --use-syn-sdc like @jenncummings the output actually had each run’s fieldmap pair applied via PEPolar SDC and none of the SyN steps were run. I.e, fieldmaps were not ignored, no SyN… difference from 21.0.2?
–When running the above command after deleting the b0FieldIdentifier/b0FieldSource from the fmap/func jsons, PEPolar SDC was still estimated, but it was just the first fieldmap pair that was applied to all runs (I guess because fmriprep noticed that the fmap data was present but no mapping was specified in the jsons). EDIT: this just seemed to estimate sdc using the first fieldmap in the html output, but the actual output images have no sdc applied.
–When running the same command after also deleting the entire fmap file directory, the SyN/fieldmapless approach was finally applied, although the output does look off-- can post about this separately.
–I also tried to do a single pass with the intention of using the PEPolar fieldmap SDC while also estimating the SyN method for comparison by specifying --use-syn-sdc and --force-syn with the fmap data present and json files including relevant pairings (no ignore command included). The resulting corrected data here was somewhat similar but not identical to the output of the first pass I mentioned above, where the run-specific fieldmaps were applied. I was expecting the output to be identical since my understanding was that the parallel/force SyN method with would be run separately and not influence the final preprocessed data, but perhaps it got incorporated somehow or caused abnormal application of the fieldmaps or there is an issue with the sequence of steps? I do see that this type of call is experimental/meant for debugging but thought I’d mention.