Fieldmap seems to be over-correcting the rest fmri

[Meishai96]

What happened?

Hi there!

My func image is in AP direction, and I am using AP/PA fieldmaps. The correction seems to go to the right direction, but also it seems to be over-correcting too much and raising some additional distortion to the image. I checked that the echo spacing and readout time were aligned between fmap and func images. I attached the screenshot.

Any help is appreciated!
Meishan

What command did you use?

singularity run --cleanenv \
    --bind ${bids_root_dir}:/data:ro \
    --bind ${out_dir}:/out \
    --bind ${work_dir}:/work \
    --bind ${FS_LICENSE}:/freesurfer_license.txt \
    /home/groups/vhenders/simg/fmriprep-23.2.3.simg \
    /data /out participant \
    --participant-label $subid \
    --fs-license-file $FS_LICENSE \
    --nthreads $nthreads \
    --stop-on-first-crash \
    --work-dir $work_dir

What version of fMRIPrep are you running?

23.1.2

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Additional information / screenshots

No response

[effigies]

Can you try with the latest version and verify this hasn't already been fixed?

[Meishai96]

I tried the fmriprep (24.1.0) but it still gave the exact same result. I will try to pull 24.1.1 today and see if that makes it better. Thanks!

[Meishai96]

Confirmed that 24.1.1 still retained the same issue. I attached another example for a better visualization (the distortion is more salient). Thank you!

[effigies]

I suppose I would check your metadata and make sure that the PhaseEncodingDirection metadata for your BOLD and fieldmaps are all correct.

I would also try running TOPUP yourself and see if you get substantially different results. It could be a limitation of the tool or the quality of the fieldmap. If there's a deviation from the TOPUP results, that's something we can look into.