In my fmriprep command I’ve been using
--force-syn, even though my data contains spin echo field maps. The documentation states that
--use-syn-sdc uses " fieldmap-free distortion correction", so is this a redundant flag option for those who are using fieldmaps for SDC (i.e. not specifying
So jsut to be clear,
--use-syn-sdc allows SyN-based SDC to be run at all, i.e., adds it to the bottom of the SDC-methods-to-try list. If any fieldmaps are available, they’ll take precedence.
--ignore fieldmaps will effectively remove everything else from that list, and thus
--use-syn-sdc --ignore fieldmaps will do just that: SyN-based SDC, ignoring fieldmaps.
--force-syn means we will always run it. This is a debugging option, and is only useful if you want to compare the quality of SyN-SDC and that of the fieldmap-based SDC, as you’ll get reports for both methods. But if you do have fieldmaps, the final result will not be affected. They’ll still be based on the fieldmaps.