fMRIPrep distortion correction issue hyperintensity in cerebellum

[jsein]

You may also want to try without the --fs-no-reconall flag, the use of this flag is somewhat discouraged, as discussed here

To use the fieldmap less option, this post will guide you:

@effigies

So just 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.

Also be aware that the use of --use-syn-sdc option along with the --ignore fieldmaps option may not work with fmriprep v20 (due to a bug that was only corrected in fmriprep v22.0.2). You may need to use --bids-filter-file to filter out the fieldmap to use the field map-less option.