Distortion correction issue related to the version of fmriprep

Summary of what happened:

Related to the discussion in other thread. I have found an issue for SDC when using the newest version (23.1.4, also 23.1.3). I’m using phase-difference B0 estimation from two close GRE sequence. However, the output from the newest version is obviously messed up. I solved this problem by changing the version back to an old version (21.0.1). However, I still think this is an issue worth discussing. I pasted the screenshot for one sample participant below. This issue is happened in all participants, so I think it should be a systematic error.

Command used

The command are kept the same across two versions.

--dummy-scans 10 \
--fd-spike-threshold 0.9 \
--fs-license-file /optnfs/freesurfer/6.0.0/license.txt \
--cifti-output 91k \
--skip-bids-validation \
--random-seed 42 \
--bold2t1w-dof 9 \
--skull-strip-fixed-seed \


Version with issues: 23.1.4
Version that works: 21.0.1

Environment (Docker, Singularity, custom installation):


Data formatted according to a validatable standard? Please provide the output of the validator:

BIDS validated

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

Hi @KeBo2023 , SDC with phase difference B0 estimation was a known weakness of fmriprep for several versions after the LTS ones (20.2.7 is the latest LTS). It is expected to be taken care of in the next release. Could you try with the pre-release 23.2.0a3?

Exemple of such reports:

and threads therein.

1 Like

Thanks @jsein . I’ll try it soon.