Increased distortions following distortion correction in FMRIPREP?

Hi all,

We have recently observed some errors with running fmriprep 23.1.4. We’ve been processing sequences with varying multi-echo factors, and there’s a protrusion that occurs primarily for single-echo sequences, so it’s like the distortion correction is increasing distortion or overcompensating. For example, here’s an image of a single-echo sequence:

Generally speaking, it looks like the effect is reduced when increasing the number of echoes, although in most cases you can still see hints at some abnormal distortion near the frontal pole and OFC regions. Here’s a multi-echo = 4 sequence, which is overall greatly reduced but still shows minor degrees of the effect:

Interestingly, this effect seems to go away when we re-run FMRIPREP and tell it to use fieldmap-free distortion correction using the --use-syn-sdc option. Here’s the same single-echo sequence from the first screenshot using the fieldmap-free approach:

I’m curious whether anyone has seen anything similar to this, and/or if anyone has any thoughts as to what might be the cause? The single-echo and multi-echo sequences are hypothetically using the same fieldmaps, so we’re a little unclear about piecing this together.

Thank you,


Hi @jimmywyngaarden ,

What kind of SDC method do you use for your data?

There has been numerous reports of difficulties of SDC with fmriprep for case 1, 2 and 3.

See for example here:

and here: